HEADER PROTEIN FIBRIL 29-MAY-21 7N2G TITLE MICROED STRUCTURE OF HUMAN CPEB3 SEGMENT(154-161) KINKED 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 7N2G 1 REMARK REVDAT 2 10-MAY-23 7N2G 1 JRNL REVDAT 1 01-JUN-22 7N2G 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 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) : 7.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.0 REMARK 3 NUMBER OF REFLECTIONS : 1360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.040 REMARK 3 FREE R VALUE TEST SET COUNT : 123 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 7.6189 - 2.5569 0.78 132 14 0.1253 0.2201 REMARK 3 2 2.5569 - 2.0424 0.81 141 13 0.1661 0.1103 REMARK 3 3 2.0424 - 1.7880 0.83 124 13 0.1750 0.2778 REMARK 3 4 1.7880 - 1.6263 0.79 108 10 0.1912 0.2402 REMARK 3 5 1.6263 - 1.5107 0.82 135 14 0.2141 0.2903 REMARK 3 6 1.5107 - 1.4222 0.84 129 13 0.2637 0.2033 REMARK 3 7 1.4222 - 1.3514 0.86 128 12 0.2524 0.2938 REMARK 3 8 1.3514 - 1.2929 0.85 117 12 0.2653 0.3258 REMARK 3 9 1.2929 - 1.2433 0.81 109 11 0.2836 0.3959 REMARK 3 10 1.2433 - 1.2010 0.85 114 11 0.3232 0.3141 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) : 24.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.52 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 7N2G 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_1000254646. 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 : 1453 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 240 RESOLUTION RANGE LOW (A) : 7.619 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 66.9 REMARK 240 DATA REDUNDANCY : 3.810 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) :1.14 REMARK 240 COMPLETENESS FOR SHELL (%) : 68.4 REMARK 240 DATA REDUNDANCY IN SHELL : 3.82 REMARK 240 R MERGE FOR SHELL (I) : 0.69700 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 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 2.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 2.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 10.24000 REMARK 290 SMTRY3 4 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: 1240 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7N2F RELATED DB: PDB REMARK 900 HUMAN CPEB3 SEGMENT(154-161) DBREF 7N2G A -2 5 PDB 7N2G 7N2G -2 5 SEQRES 1 A 8 GLN ILE GLY LEU ALA GLN THR GLN FORMUL 2 HOH *(H2 O) CRYST1 4.820 20.480 45.610 90.00 90.00 90.00 P 21 21 21 4 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 0.207469 0.000000 0.000000 0.00000 SCALE2 0.000000 0.048828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021925 0.00000 TER 124 GLN A 5 HETATM 125 O HOH A 101 7.289 10.811 3.577 1.00 10.76 O MASTER 177 0 0 0 0 0 0 6 61 1 0 1 END