HEADER PROTEIN FIBRIL 29-OCT-14 4RP7 TITLE STRUCTURE OF THE AMYLOID-FORMING SEGMENT TIITLE FROM P53 (RESIDUES TITLE 2 253-258) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TIITLE HEXAPEPTIDE SEGMENT FROM P53; COMPND 3 CHAIN: Z; COMPND 4 FRAGMENT: UNP RESIDUES 253-258; COMPND 5 SYNONYM: ANTIGEN NY-CO-13, PHOSPHOPROTEIN P53, TUMOR SUPPRESSOR P53; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CELLULAR TUMOR ANTIGEN P53 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: TIITLE(RESIDUES 253-258) FROM P53, SYNTHESIZED KEYWDS P53, AMYLOID, FIBRIL, AMYLOID-LIKE PROTOFIBRIL, P53 AGGREGATES, KEYWDS 2 POLYMER, TRANSCRIPTION FACTOR, ONCOGENE, CANCER, P53 MUTANT, PROTEIN KEYWDS 3 FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR A.B.SORIAGA,A.SORAGNI,D.EISENBERG REVDAT 3 28-FEB-24 4RP7 1 REMARK REVDAT 2 27-JAN-16 4RP7 1 JRNL REVDAT 1 13-JAN-16 4RP7 0 JRNL AUTH A.SORAGNI,D.M.JANZEN,L.M.JOHNSON,A.G.LINDGREN, JRNL AUTH 2 A.THAI-QUYNH NGUYEN,E.TIOURIN,A.B.SORIAGA,J.LU,L.JIANG, JRNL AUTH 3 K.F.FAULL,M.PELLEGRINI,S.MEMARZADEH,D.S.EISENBERG JRNL TITL A DESIGNED INHIBITOR OF P53 AGGREGATION RESCUES P53 TUMOR JRNL TITL 2 SUPPRESSION IN OVARIAN CARCINOMAS. JRNL REF CANCER CELL V. 29 90 2016 JRNL REFN ISSN 1535-6108 JRNL PMID 26748848 JRNL DOI 10.1016/J.CCELL.2015.12.002 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 635 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.240 REMARK 3 FREE R VALUE TEST SET COUNT : 65 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 0.0000 - 1.5760 0.93 570 65 0.1637 0.1925 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 80.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.40680 REMARK 3 B22 (A**2) : -0.03230 REMARK 3 B33 (A**2) : 2.19360 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.81900 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 47 REMARK 3 ANGLE : 1.861 64 REMARK 3 CHIRALITY : 0.072 11 REMARK 3 PLANARITY : 0.007 7 REMARK 3 DIHEDRAL : 10.557 17 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.5250 -0.1582 3.9867 REMARK 3 T TENSOR REMARK 3 T11: 0.0284 T22: 0.0494 REMARK 3 T33: 0.0290 T12: 0.0055 REMARK 3 T13: 0.0058 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.0034 L22: 0.2021 REMARK 3 L33: 0.0378 L12: 0.0063 REMARK 3 L13: 0.0031 L23: -0.0919 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.0003 S13: -0.0248 REMARK 3 S21: -0.0899 S22: 0.0437 S23: -0.0012 REMARK 3 S31: -0.0422 S32: 0.1216 S33: 0.0477 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 4RP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087624. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 636 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.576 REMARK 200 RESOLUTION RANGE LOW (A) : 21.494 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 17.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 0.01 M ZINC REMARK 280 CHLORIDE, 0.1 M MES BUFFER PH 6, AND 20% PEG 6000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 21.50900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.42450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.50900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.42450 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 300 REMARK: THE BIOLOGICAL UNIT IS A PAIR OF BETA SHEETS WITH THE SIDE REMARK 300 CHAINS INTERDIGITATING BETWEEN THE SHEETS. ONE SHEET IS CONSTRUCTED REMARK 300 FROM UNIT CELL TRANSLATIONS ALONG THE "B" DIRECTION (I.E. X,Y+1,Z; REMARK 300 X,Y+2,Z; X,Y+3,Z; ETC.). THE OTHER SHEET IS CONSTRUCTED FROM REMARK 300 SYMMETRY OPERATORS -X+1/2,Y+1/2,-Z+1; -X+1/2,Y+3/2,-Z+1; -X+1/2,Y+5/ REMARK 300 2,-Z+1; ETC.). 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 4.84900 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 9.69800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 14.54700 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 20.77751 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 2.42450 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 19.76047 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 20.77751 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 7.27350 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 19.76047 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 20.77751 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 12.12250 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 19.76047 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN Z 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RP6 RELATED DB: PDB DBREF 4RP7 Z 1 6 UNP P04637 P53_HUMAN 253 258 SEQRES 1 Z 6 THR ILE ILE THR LEU GLU HET ZN Z 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *2(H2 O) LINK N THR Z 1 ZN ZN Z 101 1555 1555 2.08 SITE 1 AC1 2 THR Z 1 GLU Z 6 CRYST1 43.018 4.849 19.774 90.00 92.12 90.00 C 1 2 1 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 0.023246 0.000000 0.000861 0.00000 SCALE2 0.000000 0.206228 0.000000 0.00000 SCALE3 0.000000 0.000000 0.050606 0.00000