HEADER PROTEIN FIBRIL 29-MAY-21 7N2F
TITLE MICROED STRUCTURE OF HUMAN CPEB3 SEGMENT (154-161) STRAIGHT POLYMORPH
TITLE 2 PHASED BY ARCIMBOLDO-BORGES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CPEB3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 154-161;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_TAXID: 9606
KEYWDS FUNCTIONAL AMYLOID, MICROED, AMYLOID, 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 7N2F 1 REMARK
REVDAT 2 10-MAY-23 7N2F 1 JRNL
REVDAT 1 01-JUN-22 7N2F 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. 1.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.16_3549
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) : 1.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.10
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.580
REMARK 3 COMPLETENESS FOR RANGE (%) : 78.6
REMARK 3 NUMBER OF REFLECTIONS : 1121
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.205
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.233
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.080
REMARK 3 FREE R VALUE TEST SET COUNT : 113
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 7.0970 - 2.5493 0.79 104 12 0.2096 0.3326
REMARK 3 2 2.5493 - 2.0392 0.75 107 12 0.2027 0.2301
REMARK 3 3 2.0392 - 1.7862 0.79 102 11 0.1669 0.1737
REMARK 3 4 1.7862 - 1.6250 0.76 86 10 0.1906 0.1822
REMARK 3 5 1.6250 - 1.5097 0.83 117 13 0.1811 0.2071
REMARK 3 6 1.5097 - 1.4215 0.81 108 12 0.2187 0.2942
REMARK 3 7 1.4215 - 1.3508 0.78 100 12 0.2461 0.2215
REMARK 3 8 1.3508 - 1.2923 0.77 95 10 0.2173 0.1769
REMARK 3 9 1.2923 - 1.2429 0.81 93 11 0.2008 0.1658
REMARK 3 10 1.2429 - 1.2002 0.79 96 10 0.2119 0.1785
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.680
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 8.28
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.12
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 7N2F 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_1000254793.
REMARK 240
REMARK 240 EXPERIMENTAL DETAILS
REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY
REMARK 240 SAMPLE TYPE : FILAMENT
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 : OTHER
REMARK 240 ACCELERATION VOLTAGE (KV) : 200
REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1130
REMARK 240 RESOLUTION RANGE HIGH (A) : 1.200
REMARK 240 RESOLUTION RANGE LOW (A) : 7.097
REMARK 240 DATA SCALING SOFTWARE : XSCALE
REMARK 240 COMPLETENESS FOR RANGE (%) : 78.7
REMARK 240 DATA REDUNDANCY : 5.690
REMARK 240 IN THE HIGHEST RESOLUTION SHELL
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.20
REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.26
REMARK 240 COMPLETENESS FOR SHELL (%) : 79.2
REMARK 240 DATA REDUNDANCY IN SHELL : 5.09
REMARK 240 R MERGE FOR SHELL (I) : 0.18700
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 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 8.14500
REMARK 290 SMTRY3 2 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: 1260 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 7N2F A 1 8 PDB 7N2F 7N2F 1 8
SEQRES 1 A 8 GLN ILE GLY LEU ALA GLN THR GLN
CRYST1 4.830 16.290 29.020 90.00 94.61 90.00 P 1 21 1 2
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 0.207039 0.000000 0.016676 0.00000
SCALE2 0.000000 0.061387 0.000000 0.00000
SCALE3 0.000000 0.000000 0.034571 0.00000
ATOM 1 N GLN A 1 1.383 2.535 -11.000 1.00 4.70 N
ATOM 2 CA GLN A 1 1.543 3.509 -9.926 1.00 4.07 C
ATOM 3 C GLN A 1 0.885 2.969 -8.661 1.00 3.03 C
ATOM 4 O GLN A 1 -0.334 2.814 -8.619 1.00 4.99 O
ATOM 5 CB GLN A 1 0.939 4.865 -10.330 1.00 4.05 C
ATOM 6 CG GLN A 1 1.230 6.022 -9.378 1.00 5.69 C
ATOM 7 CD GLN A 1 0.613 7.323 -9.846 1.00 2.73 C
ATOM 8 OE1 GLN A 1 -0.600 7.473 -9.843 1.00 4.36 O
ATOM 9 NE2 GLN A 1 1.448 8.270 -10.254 1.00 5.00 N
ATOM 10 N ILE A 2 1.690 2.663 -7.643 1.00 2.03 N
ATOM 11 CA ILE A 2 1.205 2.187 -6.351 1.00 1.85 C
ATOM 12 C ILE A 2 1.819 3.040 -5.251 1.00 0.00 C
ATOM 13 O ILE A 2 3.041 3.209 -5.206 1.00 0.17 O
ATOM 14 CB ILE A 2 1.552 0.705 -6.108 1.00 0.67 C
ATOM 15 CG1 ILE A 2 0.858 -0.212 -7.120 1.00 3.56 C
ATOM 16 CG2 ILE A 2 1.179 0.313 -4.678 1.00 0.93 C
ATOM 17 CD1 ILE A 2 1.149 -1.694 -6.885 1.00 4.22 C
ATOM 18 N GLY A 3 0.974 3.553 -4.354 1.00 2.69 N
ATOM 19 CA GLY A 3 1.401 4.254 -3.154 1.00 2.19 C
ATOM 20 C GLY A 3 0.828 3.577 -1.928 1.00 0.14 C
ATOM 21 O GLY A 3 -0.393 3.424 -1.831 1.00 1.57 O
ATOM 22 N ALEU A 4 1.681 3.172 -0.986 0.53 1.06 N
ATOM 23 N BLEU A 4 1.688 3.174 -0.995 0.47 1.06 N
ATOM 24 CA ALEU A 4 1.268 2.390 0.176 0.53 1.21 C
ATOM 25 CA BLEU A 4 1.296 2.396 0.174 0.47 1.21 C
ATOM 26 C ALEU A 4 1.896 2.990 1.426 0.53 0.89 C
ATOM 27 C BLEU A 4 1.906 3.055 1.403 0.47 0.88 C
ATOM 28 O ALEU A 4 3.123 2.981 1.566 0.53 1.54 O
ATOM 29 O BLEU A 4 3.132 3.161 1.500 0.47 1.56 O
ATOM 30 CB ALEU A 4 1.699 0.926 0.004 0.53 2.61 C
ATOM 31 CB BLEU A 4 1.807 0.955 0.028 0.47 2.63 C
ATOM 32 CG ALEU A 4 1.551 -0.044 1.179 0.53 6.31 C
ATOM 33 CG BLEU A 4 1.070 -0.191 0.721 0.47 3.75 C
ATOM 34 CD1ALEU A 4 0.130 -0.060 1.713 0.53 3.05 C
ATOM 35 CD1BLEU A 4 1.404 -1.526 0.057 0.47 1.51 C
ATOM 36 CD2ALEU A 4 1.984 -1.444 0.756 0.53 2.00 C
ATOM 37 CD2BLEU A 4 1.434 -0.221 2.191 0.47 3.74 C
ATOM 38 N ALA A 5 1.058 3.499 2.334 1.00 1.29 N
ATOM 39 CA ALA A 5 1.506 4.185 3.542 1.00 1.82 C
ATOM 40 C ALA A 5 0.878 3.534 4.766 1.00 0.66 C
ATOM 41 O ALA A 5 -0.347 3.366 4.812 1.00 1.29 O
ATOM 42 CB ALA A 5 1.124 5.671 3.502 1.00 2.29 C
ATOM 43 N GLN A 6 1.705 3.190 5.761 1.00 1.07 N
ATOM 44 CA GLN A 6 1.241 2.477 6.948 1.00 2.12 C
ATOM 45 C GLN A 6 1.856 3.064 8.210 1.00 0.24 C
ATOM 46 O GLN A 6 3.067 3.296 8.261 1.00 1.47 O
ATOM 47 CB GLN A 6 1.629 0.990 6.882 1.00 2.54 C
ATOM 48 CG GLN A 6 1.143 0.233 5.661 1.00 2.78 C
ATOM 49 CD GLN A 6 1.696 -1.190 5.620 1.00 1.36 C
ATOM 50 OE1 GLN A 6 2.905 -1.386 5.564 1.00 2.75 O
ATOM 51 NE2 GLN A 6 0.811 -2.183 5.659 1.00 5.04 N
ATOM 52 N ATHR A 7 1.026 3.233 9.246 0.62 2.36 N
ATOM 53 N BTHR A 7 1.025 3.293 9.231 0.38 2.38 N
ATOM 54 CA ATHR A 7 1.450 3.780 10.529 0.62 3.49 C
ATOM 55 CA BTHR A 7 1.492 3.751 10.533 0.38 3.52 C
ATOM 56 C ATHR A 7 0.811 3.005 11.672 0.62 2.70 C
ATOM 57 C BTHR A 7 0.837 2.947 11.645 0.38 2.70 C
ATOM 58 O ATHR A 7 -0.378 2.679 11.621 0.62 3.11 O
ATOM 59 O BTHR A 7 -0.324 2.539 11.543 0.38 3.66 O
ATOM 60 CB ATHR A 7 1.033 5.253 10.670 0.62 5.60 C
ATOM 61 CB BTHR A 7 1.193 5.245 10.796 0.38 5.63 C
ATOM 62 OG1ATHR A 7 1.350 5.968 9.470 0.62 8.30 O
ATOM 63 OG1BTHR A 7 -0.219 5.473 10.761 0.38 2.27 O
ATOM 64 CG2ATHR A 7 1.750 5.897 11.844 0.62 7.25 C
ATOM 65 CG2BTHR A 7 1.863 6.127 9.775 0.38 7.90 C
ATOM 66 N GLN A 8 1.589 2.744 12.720 1.00 4.34 N
ATOM 67 CA GLN A 8 1.045 2.160 13.947 1.00 5.10 C
ATOM 68 C GLN A 8 1.801 2.661 15.176 1.00 6.42 C
ATOM 69 O GLN A 8 1.379 2.437 16.311 1.00 11.37 O
ATOM 70 CB GLN A 8 1.040 0.627 13.898 1.00 6.95 C
ATOM 71 CG GLN A 8 2.414 -0.044 13.930 1.00 10.41 C
ATOM 72 CD GLN A 8 2.325 -1.563 13.828 1.00 12.90 C
ATOM 73 OE1 GLN A 8 1.233 -2.125 13.780 1.00 35.11 O
ATOM 74 NE2 GLN A 8 3.475 -2.230 13.796 1.00 12.48 N
ATOM 75 OXT GLN A 8 2.852 3.290 15.061 1.00 6.53 O
TER 76 GLN A 8
MASTER 165 0 0 0 0 0 0 6 60 1 0 1
END