HEADER PROTEIN FIBRIL 29-MAY-21 7N2J
TITLE MICROED STRUCTURE OF A MUTANT MAMMALIAN PRION SEGMENT PHASED BY
TITLE 2 ARCIMBOLDO-BORGES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PRION PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS PRION, MICROED, AMYLOID, PROTEIN FIBRIL
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR L.S.RICHARDS,M.D.FLORES,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA
REVDAT 3 22-MAY-24 7N2J 1 REMARK
REVDAT 2 10-MAY-23 7N2J 1 JRNL
REVDAT 1 01-JUN-22 7N2J 0
JRNL AUTH L.S.RICHARDS,M.D.FLORES,C.MILLAN,C.GLYNN,C.T.ZEE,M.R.SAWAYA,
JRNL AUTH 2 M.GALLAGHER-JONES,R.J.BORGES,I.USON,J.A.RODRIGUEZ
JRNL TITL FRAGMENT-BASED AB INITIO PHASING OF PEPTIDIC NANOCRYSTALS BY
JRNL TITL 2 MICROED.
JRNL REF ACS BIO MED CHEM AU V. 3 201 2023
JRNL REFN ESSN 2694-2437
JRNL PMID 37096030
JRNL DOI 10.1021/ACSBIOMEDCHEMAU.2C00082
REMARK 2
REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.98
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.240
REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4
REMARK 3 NUMBER OF REFLECTIONS : 730
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.174
REMARK 3 FREE R VALUE : 0.227
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.040
REMARK 3 FREE R VALUE TEST SET COUNT : 66
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 7.9800 - 3.1707 0.80 67 7 0.1345 0.1855
REMARK 3 2 3.1707 - 2.5434 0.80 51 5 0.2068 0.2019
REMARK 3 3 2.5434 - 2.2300 0.85 84 8 0.1603 0.1674
REMARK 3 4 2.2300 - 2.0297 0.78 62 7 0.1492 0.1924
REMARK 3 5 2.0297 - 1.8863 0.81 74 7 0.1591 0.3424
REMARK 3 6 1.8863 - 1.7764 0.80 59 6 0.2183 0.4625
REMARK 3 7 1.7764 - 1.6883 0.79 56 5 0.2150 0.3783
REMARK 3 8 1.6883 - 1.6155 0.86 64 7 0.2121 0.2802
REMARK 3 9 1.6155 - 1.5537 0.79 78 7 0.1859 0.1276
REMARK 3 10 1.5537 - 1.5005 0.81 69 7 0.2290 0.1879
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.410
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 6.86
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.56
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7N2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21.
REMARK 100 THE DEPOSITION ID IS D_1000254652.
REMARK 240
REMARK 240 EXPERIMENTAL DETAILS
REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY
REMARK 240 SAMPLE TYPE : 3D ARRAY
REMARK 240 SPECIMEN TYPE : NULL
REMARK 240 DATA ACQUISITION
REMARK 240 DATE OF DATA COLLECTION : NULL
REMARK 240 TEMPERATURE (KELVIN) : NULL
REMARK 240 PH : NULL
REMARK 240 NUMBER OF CRYSTALS USED : NULL
REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA
REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K)
REMARK 240 ACCELERATION VOLTAGE (KV) : 200
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 915
REMARK 240 RESOLUTION RANGE HIGH (A) : 0.900
REMARK 240 RESOLUTION RANGE LOW (A) : 7.980
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 81.0
REMARK 240 DATA REDUNDANCY : 5.383
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :0.90
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :0.92
REMARK 240 COMPLETENESS FOR SHELL (%) : 81.1
REMARK 240 DATA REDUNDANCY IN SHELL : 4.78
REMARK 240 R MERGE FOR SHELL (I) : 0.46600
REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 240 SOFTWARE USED : NULL
REMARK 240 STARTING MODEL : NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 1380 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
DBREF 7N2J A -1 7 PDB 7N2J 7N2J -1 7
SEQRES 1 A 9 GLN TYR ASN ASN GLU ASN ASN PHE VAL
FORMUL 2 HOH *(H2 O)
CRYST1 4.870 10.060 30.660 94.85 90.26 99.99 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.205339 0.036162 0.004095 0.00000
SCALE2 0.000000 0.100933 0.008780 0.00000
SCALE3 0.000000 0.000000 0.032739 0.00000
ATOM 1 N GLN A -1 -0.029 -6.868 -4.770 1.00 6.62 N
ATOM 2 CA GLN A -1 0.488 -5.893 -3.826 1.00 3.95 C
ATOM 3 C GLN A -1 -0.178 -5.999 -2.457 1.00 5.01 C
ATOM 4 O GLN A -1 -1.403 -6.045 -2.357 1.00 7.77 O
ATOM 5 CB GLN A -1 0.310 -4.483 -4.391 1.00 6.79 C
ATOM 6 CG GLN A -1 1.099 -3.411 -3.683 1.00 6.21 C
ATOM 7 CD GLN A -1 0.738 -2.052 -4.207 1.00 5.72 C
ATOM 8 OE1 GLN A -1 -0.407 -1.611 -4.080 1.00 8.20 O
ATOM 9 NE2 GLN A -1 1.702 -1.381 -4.820 1.00 8.87 N
ATOM 10 N TYR A 0 0.642 -6.004 -1.409 1.00 1.70 N
ATOM 11 CA TYR A 0 0.201 -6.154 -0.026 1.00 1.71 C
ATOM 12 C TYR A 0 0.629 -4.917 0.756 1.00 2.21 C
ATOM 13 O TYR A 0 1.818 -4.596 0.797 1.00 1.96 O
ATOM 14 CB TYR A 0 0.814 -7.433 0.560 1.00 2.07 C
ATOM 15 CG TYR A 0 0.452 -7.785 1.983 1.00 1.44 C
ATOM 16 CD1 TYR A 0 -0.557 -8.713 2.248 1.00 0.92 C
ATOM 17 CD2 TYR A 0 1.156 -7.244 3.061 1.00 1.07 C
ATOM 18 CE1 TYR A 0 -0.884 -9.071 3.545 1.00 0.52 C
ATOM 19 CE2 TYR A 0 0.833 -7.595 4.371 1.00 1.68 C
ATOM 20 CZ TYR A 0 -0.184 -8.517 4.600 1.00 0.00 C
ATOM 21 OH TYR A 0 -0.520 -8.883 5.887 1.00 1.06 O
ATOM 22 N ASN A 1 -0.335 -4.216 1.363 1.00 2.98 N
ATOM 23 CA ASN A 1 -0.068 -2.956 2.062 1.00 1.63 C
ATOM 24 C ASN A 1 -0.647 -3.029 3.469 1.00 1.09 C
ATOM 25 O ASN A 1 -1.854 -3.234 3.632 1.00 1.37 O
ATOM 26 CB ASN A 1 -0.660 -1.751 1.317 1.00 0.93 C
ATOM 27 CG ASN A 1 -0.173 -1.646 -0.108 1.00 3.14 C
ATOM 28 OD1 ASN A 1 1.014 -1.473 -0.357 1.00 5.15 O
ATOM 29 ND2 ASN A 1 -1.097 -1.752 -1.058 1.00 5.80 N
ATOM 30 N ASN A 2 0.200 -2.827 4.479 1.00 0.73 N
ATOM 31 CA ASN A 2 -0.240 -2.965 5.862 1.00 1.09 C
ATOM 32 C ASN A 2 0.515 -1.982 6.744 1.00 1.36 C
ATOM 33 O ASN A 2 1.532 -1.402 6.346 1.00 0.66 O
ATOM 34 CB ASN A 2 -0.050 -4.408 6.372 1.00 0.20 C
ATOM 35 CG ASN A 2 -1.231 -4.894 7.170 1.00 1.68 C
ATOM 36 OD1 ASN A 2 -1.835 -4.131 7.916 1.00 2.63 O
ATOM 37 ND2 ASN A 2 -1.593 -6.167 6.995 1.00 0.58 N
ATOM 38 N GLU A 3 -0.015 -1.790 7.952 1.00 0.42 N
ATOM 39 CA GLU A 3 0.660 -1.014 8.979 1.00 1.39 C
ATOM 40 C GLU A 3 0.224 -1.542 10.333 1.00 0.36 C
ATOM 41 O GLU A 3 -0.915 -1.980 10.496 1.00 1.40 O
ATOM 42 CB GLU A 3 0.354 0.484 8.855 1.00 1.06 C
ATOM 43 CG GLU A 3 -1.086 0.862 9.210 1.00 2.06 C
ATOM 44 CD GLU A 3 -1.277 2.358 9.448 1.00 4.03 C
ATOM 45 OE1 GLU A 3 -0.695 3.169 8.700 1.00 4.66 O
ATOM 46 OE2 GLU A 3 -2.012 2.730 10.387 1.00 1.92 O
ATOM 47 N ASN A 4 1.146 -1.530 11.295 1.00 1.13 N
ATOM 48 CA ASN A 4 0.857 -2.053 12.627 1.00 2.58 C
ATOM 49 C ASN A 4 1.530 -1.173 13.666 1.00 3.03 C
ATOM 50 O ASN A 4 2.761 -1.062 13.683 1.00 2.41 O
ATOM 51 CB ASN A 4 1.322 -3.515 12.772 1.00 1.31 C
ATOM 52 CG ASN A 4 0.867 -4.389 11.621 1.00 1.33 C
ATOM 53 OD1 ASN A 4 -0.276 -4.830 11.587 1.00 3.79 O
ATOM 54 ND2 ASN A 4 1.763 -4.641 10.665 1.00 2.52 N
ATOM 55 N ASN A 5 0.731 -0.554 14.533 1.00 3.27 N
ATOM 56 CA ASN A 5 1.241 0.307 15.590 1.00 4.40 C
ATOM 57 C ASN A 5 0.714 -0.190 16.923 1.00 4.49 C
ATOM 58 O ASN A 5 -0.493 -0.375 17.081 1.00 3.51 O
ATOM 59 CB ASN A 5 0.833 1.767 15.365 1.00 4.65 C
ATOM 60 CG ASN A 5 1.388 2.336 14.067 1.00 5.43 C
ATOM 61 OD1 ASN A 5 0.641 2.773 13.189 1.00 8.31 O
ATOM 62 ND2 ASN A 5 2.706 2.320 13.938 1.00 4.91 N
ATOM 63 N PHE A 6 1.614 -0.384 17.884 1.00 3.36 N
ATOM 64 CA PHE A 6 1.255 -0.881 19.210 1.00 5.58 C
ATOM 65 C PHE A 6 1.720 0.137 20.244 1.00 6.45 C
ATOM 66 O PHE A 6 2.923 0.372 20.391 1.00 6.07 O
ATOM 67 CB PHE A 6 1.878 -2.254 19.468 1.00 5.37 C
ATOM 68 CG PHE A 6 1.501 -3.304 18.442 1.00 6.63 C
ATOM 69 CD1 PHE A 6 0.465 -4.192 18.679 1.00 6.87 C
ATOM 70 CD2 PHE A 6 2.198 -3.410 17.246 1.00 5.24 C
ATOM 71 CE1 PHE A 6 0.128 -5.165 17.743 1.00 5.21 C
ATOM 72 CE2 PHE A 6 1.853 -4.375 16.308 1.00 9.54 C
ATOM 73 CZ PHE A 6 0.813 -5.251 16.561 1.00 4.25 C
ATOM 74 N VAL A 7 0.773 0.755 20.944 1.00 8.45 N
ATOM 75 CA VAL A 7 1.100 1.743 21.972 1.00 10.91 C
ATOM 76 C VAL A 7 0.351 1.433 23.258 1.00 21.56 C
ATOM 77 O VAL A 7 0.776 1.873 24.325 1.00 23.19 O
ATOM 78 CB VAL A 7 0.785 3.176 21.515 1.00 12.52 C
ATOM 79 CG1 VAL A 7 1.553 4.178 22.363 1.00 14.42 C
ATOM 80 CG2 VAL A 7 1.124 3.352 20.052 1.00 14.63 C
ATOM 81 OXT VAL A 7 -0.682 0.753 23.262 1.00 16.75 O
TER 82 VAL A 7
HETATM 83 O HOH A 101 1.310 0.962 -1.663 1.00 5.73 O
MASTER 161 0 0 0 0 0 0 6 82 1 0 1
END