HEADER PROTEIN FIBRIL 29-MAY-21 7N2K
TITLE MICROED STRUCTURE OF SEQUENCE VARIANT OF REPEAT SEGMENT OF THE YEAST
TITLE 2 PRION NEW1P PHASED BY ARCIMBOLDO-BORGES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PRION NEW1P;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: REPEAT SEGMENT;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 4 ORGANISM_TAXID: 4932
KEYWDS AMYLOID, MICROED, PRION, YEAST, NEW1P, PROTEIN FIBRIL
EXPDTA ELECTRON CRYSTALLOGRAPHY
AUTHOR M.D.FLORES,L.S.RICHARDS,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA
REVDAT 3 22-MAY-24 7N2K 1 REMARK
REVDAT 2 10-MAY-23 7N2K 1 JRNL
REVDAT 1 01-JUN-22 7N2K 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. 1.30 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) : 1.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.60
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.230
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9
REMARK 3 NUMBER OF REFLECTIONS : 969
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.164
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.185
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010
REMARK 3 FREE R VALUE TEST SET COUNT : 97
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 13.6000 - 2.7958 0.99 84 10 0.1228 0.1032
REMARK 3 2 2.7958 - 2.2222 1.00 88 10 0.1488 0.1450
REMARK 3 3 2.2222 - 1.9422 1.00 93 10 0.1499 0.1815
REMARK 3 4 1.9422 - 1.7651 1.00 87 10 0.1338 0.2253
REMARK 3 5 1.7651 - 1.6388 1.00 78 8 0.1554 0.4104
REMARK 3 6 1.6388 - 1.5423 1.00 93 11 0.1965 0.1744
REMARK 3 7 1.5423 - 1.4652 1.00 96 10 0.1766 0.2370
REMARK 3 8 1.4652 - 1.4014 1.00 90 10 0.2742 0.2141
REMARK 3 9 1.4014 - 1.3475 0.92 84 10 0.2561 0.2343
REMARK 3 10 1.3475 - 1.3011 0.88 79 8 0.2274 0.3074
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) : 0.140
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.830
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 11.19
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.21
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 7N2K 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_1000254650.
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 : 1357
REMARK 240 RESOLUTION RANGE HIGH (A) : 1.100
REMARK 240 RESOLUTION RANGE LOW (A) : 13.600
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 83.4
REMARK 240 DATA REDUNDANCY : 5.817
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.10
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.19
REMARK 240 COMPLETENESS FOR SHELL (%) : 53.2
REMARK 240 DATA REDUNDANCY IN SHELL : 2.26
REMARK 240 R MERGE FOR SHELL (I) : 0.48300
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 31
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 1.61000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 3.22000
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: 1010 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 7N2K A 1 6 PDB 7N2K 7N2K 1 6
SEQRES 1 A 6 ASN TYR ASN ASN TYR GLN
FORMUL 2 HOH *3(H2 O)
CRYST1 27.200 27.200 4.830 90.00 90.00 120.00 P 31 3
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 0.036765 0.021226 0.000000 0.00000
SCALE2 0.000000 0.042452 0.000000 0.00000
SCALE3 0.000000 0.000000 0.207039 0.00000
ATOM 1 N ASN A 1 22.369 5.744 1.094 1.00 7.07 N
ATOM 2 CA ASN A 1 21.081 5.597 0.427 1.00 4.81 C
ATOM 3 C ASN A 1 19.985 6.337 1.176 1.00 4.87 C
ATOM 4 O ASN A 1 19.911 6.283 2.404 1.00 4.58 O
ATOM 5 CB ASN A 1 20.705 4.120 0.277 1.00 6.92 C
ATOM 6 CG ASN A 1 21.608 3.376 -0.712 1.00 8.52 C
ATOM 7 OD1 ASN A 1 22.486 3.968 -1.343 1.00 10.10 O
ATOM 8 ND2 ASN A 1 21.385 2.081 -0.848 1.00 8.89 N
ATOM 9 N TYR A 2 19.133 7.037 0.431 1.00 3.79 N
ATOM 10 CA TYR A 2 18.017 7.774 1.017 1.00 3.44 C
ATOM 11 C TYR A 2 18.476 8.796 2.049 1.00 3.55 C
ATOM 12 O TYR A 2 17.754 9.081 2.990 1.00 4.02 O
ATOM 13 CB TYR A 2 16.946 6.847 1.599 1.00 3.13 C
ATOM 14 CG TYR A 2 16.408 5.869 0.583 1.00 3.49 C
ATOM 15 CD1 TYR A 2 15.254 6.155 -0.161 1.00 3.72 C
ATOM 16 CD2 TYR A 2 17.051 4.653 0.355 1.00 2.94 C
ATOM 17 CE1 TYR A 2 14.753 5.251 -1.108 1.00 2.49 C
ATOM 18 CE2 TYR A 2 16.556 3.739 -0.586 1.00 3.92 C
ATOM 19 CZ TYR A 2 15.404 4.043 -1.309 1.00 3.93 C
ATOM 20 OH TYR A 2 14.931 3.146 -2.242 1.00 4.12 O
ATOM 21 N ASN A 3 19.679 9.349 1.874 1.00 4.04 N
ATOM 22 CA ASN A 3 20.187 10.413 2.731 1.00 5.20 C
ATOM 23 C ASN A 3 19.833 11.778 2.150 1.00 4.91 C
ATOM 24 O ASN A 3 19.819 11.967 0.928 1.00 5.39 O
ATOM 25 CB ASN A 3 21.713 10.320 2.865 1.00 4.09 C
ATOM 26 CG ASN A 3 22.161 9.053 3.561 1.00 3.50 C
ATOM 27 OD1 ASN A 3 21.661 8.715 4.624 1.00 4.17 O
ATOM 28 ND2 ASN A 3 23.110 8.348 2.964 1.00 5.61 N
ATOM 29 N ASN A 4 19.582 12.742 3.038 1.00 4.54 N
ATOM 30 CA ASN A 4 19.134 14.077 2.660 1.00 4.93 C
ATOM 31 C ASN A 4 20.145 15.116 3.117 1.00 4.47 C
ATOM 32 O ASN A 4 20.473 15.179 4.303 1.00 6.47 O
ATOM 33 CB ASN A 4 17.784 14.384 3.308 1.00 5.35 C
ATOM 34 CG ASN A 4 17.239 15.717 2.880 1.00 4.66 C
ATOM 35 OD1 ASN A 4 17.170 16.663 3.662 1.00 7.36 O
ATOM 36 ND2 ASN A 4 16.865 15.810 1.619 1.00 7.63 N
ATOM 37 N TYR A 5 20.624 15.940 2.183 1.00 6.40 N
ATOM 38 CA TYR A 5 21.538 17.037 2.489 1.00 6.80 C
ATOM 39 C TYR A 5 20.920 18.310 1.936 1.00 6.81 C
ATOM 40 O TYR A 5 20.729 18.434 0.725 1.00 9.22 O
ATOM 41 CB TYR A 5 22.919 16.804 1.861 1.00 8.60 C
ATOM 42 CG TYR A 5 23.506 15.430 2.138 1.00 8.64 C
ATOM 43 CD1 TYR A 5 24.432 15.241 3.165 1.00 11.81 C
ATOM 44 CD2 TYR A 5 23.132 14.320 1.381 1.00 8.81 C
ATOM 45 CE1 TYR A 5 24.969 13.985 3.431 1.00 9.93 C
ATOM 46 CE2 TYR A 5 23.667 13.058 1.634 1.00 7.85 C
ATOM 47 CZ TYR A 5 24.586 12.900 2.657 1.00 9.06 C
ATOM 48 OH TYR A 5 25.114 11.649 2.919 1.00 11.26 O
ATOM 49 N GLN A 6 20.579 19.240 2.815 1.00 8.95 N
ATOM 50 CA GLN A 6 19.903 20.443 2.364 1.00 9.37 C
ATOM 51 C GLN A 6 20.391 21.670 3.111 1.00 10.61 C
ATOM 52 O GLN A 6 20.040 22.795 2.751 1.00 10.30 O
ATOM 53 CB GLN A 6 18.401 20.291 2.559 1.00 10.35 C
ATOM 54 CG GLN A 6 18.006 20.244 4.007 1.00 11.31 C
ATOM 55 CD GLN A 6 16.502 20.307 4.219 1.00 12.98 C
ATOM 56 OE1 GLN A 6 16.001 21.164 4.947 1.00 14.24 O
ATOM 57 NE2 GLN A 6 15.779 19.394 3.589 1.00 11.39 N
ATOM 58 OXT GLN A 6 21.133 21.570 4.086 1.00 9.75 O
TER 59 GLN A 6
HETATM 60 O HOH A 101 25.112 10.153 1.079 1.00 10.99 O
HETATM 61 O HOH A 102 17.806 23.166 1.286 1.00 15.90 O
HETATM 62 O HOH A 103 13.103 21.040 5.211 1.00 18.07 O
MASTER 169 0 0 0 0 0 0 6 61 1 0 1
END