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