PDB Short entry for 4FZ3 HEADER HYDROLASE/HYDROLASE SUBSTRATE 06-JUL-12 4FZ3 TITLE CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH ACETYL P53 PEPTIDE COUPLED TITLE 2 WITH 4-AMINO-7-METHYLCOUMARIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 118-399; COMPND 5 SYNONYM: HSIRT3, REGULATORY PROTEIN SIR2 HOMOLOG 3, SIR2-LIKE PROTEIN COMPND 6 3; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE FROM CELLULAR TUMOR ANTIGEN P53; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SIRT3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS ZINC-BINDING MOTIF, ROSSMANN FOLD, NAD-DEPENDENT DEACETYLASE, KEYWDS 2 MITOCHONDRIAL, HYDROLASE-HYDROLASE SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.LIU,J.WU,D.ZHANG,K.CHEN,H.JIANG,H.LIU REVDAT 3 06-DEC-23 4FZ3 1 LINK REVDAT 2 08-NOV-23 4FZ3 1 REMARK SEQADV LINK REVDAT 1 20-MAR-13 4FZ3 0 JRNL AUTH J.WU,D.ZHANG,L.CHEN,J.LI,J.WANG,C.NING,N.YU,F.ZHAO,D.CHEN, JRNL AUTH 2 X.CHEN,K.CHEN,H.JIANG,H.LIU,D.LIU JRNL TITL DISCOVERY AND MECHANISM STUDY OF SIRT1 ACTIVATORS THAT JRNL TITL 2 PROMOTE THE DEACETYLATION OF FLUOROPHORE-LABELED SUBSTRATE JRNL REF J.MED.CHEM. V. 56 761 2013 JRNL REFN ISSN 0022-2623 JRNL PMID 23316803 JRNL DOI 10.1021/JM301032J REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.400 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17380 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2109 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 163 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) : 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4FZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17380 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 77.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3GLS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.85M HEPES-NA, 8.5%(V/V) ISO REMARK 280 -PROPANOL, 17%(W/V) PEG4000, 15%(V/V) GLYCEROL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 57.40450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.14250 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.06733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 57.40450 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 33.14250 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.06733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 57.40450 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 33.14250 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.06733 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 57.40450 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 33.14250 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.06733 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 57.40450 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 33.14250 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 41.06733 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 57.40450 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 33.14250 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 41.06733 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.28501 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 82.13467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 66.28501 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 82.13467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 66.28501 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 82.13467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 66.28501 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 82.13467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 66.28501 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 82.13467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 66.28501 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 82.13467 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1076 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1122 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1143 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 117 REMARK 465 SER A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 GLY A 121 REMARK 465 ARG A 158 REMARK 465 SER A 159 REMARK 465 PRO A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 GLY A 163 REMARK 465 LEU A 164 REMARK 465 TYR A 165 REMARK 465 SER A 166 REMARK 465 ASN A 167 REMARK 465 GLY A 392 REMARK 465 LYS A 393 REMARK 465 LEU A 394 REMARK 465 ASP A 395 REMARK 465 GLY A 396 REMARK 465 PRO A 397 REMARK 465 ASP A 398 REMARK 465 LYS A 399 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 200 O HOH A 1049 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN A 388 CG GLN A 388 CD 0.186 REMARK 500 LYS B 803 C ALY B 804 N 0.248 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 801 C - N - CA ANGL. DEV. = -23.4 DEGREES REMARK 500 ARG B 801 CG - CD - NE ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG B 801 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 138 13.81 -142.55 REMARK 500 ARG A 139 74.11 -118.59 REMARK 500 TYR A 171 2.35 -65.39 REMARK 500 THR A 284 -0.42 78.75 REMARK 500 ASP A 290 46.98 -81.12 REMARK 500 SER A 336 -27.02 -39.22 REMARK 500 HIS B 802 109.88 -55.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 259 SG 105.5 REMARK 620 3 CYS A 280 SG 109.7 111.7 REMARK 620 4 CYS A 283 SG 94.8 117.2 115.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 DBREF 4FZ3 A 118 399 UNP Q9NTG7 SIR3_HUMAN 118 399 DBREF 4FZ3 B 801 804 UNP P04637 P53_HUMAN 379 382 SEQADV 4FZ3 GLY A 117 UNP Q9NTG7 EXPRESSION TAG SEQADV 4FZ3 ACE B 800 UNP P04637 ACETYLATION SEQADV 4FZ3 MCM B 805 UNP P04637 AMIDATION SEQRES 1 A 283 GLY SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL ALA SEQRES 2 A 283 GLU LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL VAL SEQRES 3 A 283 MET VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE PRO SEQRES 4 A 283 ASP PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN LEU SEQRES 5 A 283 GLN GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE GLU SEQRES 6 A 283 LEU PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE THR SEQRES 7 A 283 LEU ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO ASN SEQRES 8 A 283 VAL THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS GLY SEQRES 9 A 283 LEU LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY LEU SEQRES 10 A 283 GLU ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL GLU SEQRES 11 A 283 ALA HIS GLY THR PHE ALA SER ALA THR CYS THR VAL CYS SEQRES 12 A 283 GLN ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP VAL SEQRES 13 A 283 MET ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR GLY SEQRES 14 A 283 VAL VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO LEU SEQRES 15 A 283 PRO GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO MET SEQRES 16 A 283 ALA ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU VAL SEQRES 17 A 283 GLU PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SER SEQRES 18 A 283 VAL PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY PRO SEQRES 19 A 283 LEU ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN LEU SEQRES 20 A 283 GLY ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU LEU SEQRES 21 A 283 LEU GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN ARG SEQRES 22 A 283 GLU THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 B 6 ACE ARG HIS LYS ALY MCM MODRES 4FZ3 ALY B 804 LYS N(6)-ACETYLLYSINE HET ACE B 800 3 HET ALY B 804 12 HET MCM B 805 13 HET ZN A 401 1 HETNAM ACE ACETYL GROUP HETNAM ALY N(6)-ACETYLLYSINE HETNAM MCM 7-AMINO-4-METHYL-CHROMEN-2-ONE HETNAM ZN ZINC ION HETSYN MCM 7-AMINO-4-METHYLCOUMARIN FORMUL 2 ACE C2 H4 O FORMUL 2 ALY C8 H16 N2 O3 FORMUL 2 MCM C10 H9 N O2 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *163(H2 O) HELIX 1 1 SER A 124 ALA A 134 1 11 HELIX 2 2 ALA A 146 GLY A 153 5 8 HELIX 3 3 TYR A 175 PHE A 180 5 6 HELIX 4 4 GLU A 181 ASN A 188 1 8 HELIX 5 5 PRO A 189 TYR A 200 1 12 HELIX 6 6 ASN A 207 LYS A 219 1 13 HELIX 7 7 GLY A 232 SER A 237 1 6 HELIX 8 8 PRO A 240 SER A 242 5 3 HELIX 9 9 GLY A 265 ALA A 274 1 10 HELIX 10 10 PRO A 299 LEU A 303 5 5 HELIX 11 11 LEU A 304 ALA A 312 1 9 HELIX 12 12 PRO A 326 THR A 331 1 6 HELIX 13 13 GLY A 349 HIS A 354 1 6 HELIX 14 14 ASP A 365 GLY A 378 1 14 HELIX 15 15 TRP A 379 THR A 391 1 13 SHEET 1 A 6 LEU A 244 GLU A 246 0 SHEET 2 A 6 LEU A 222 THR A 227 1 N THR A 227 O VAL A 245 SHEET 3 A 6 VAL A 140 VAL A 144 1 N VAL A 142 O TYR A 226 SHEET 4 A 6 LEU A 314 LEU A 318 1 O LEU A 318 N MET A 143 SHEET 5 A 6 ARG A 340 ASN A 344 1 O LEU A 341 N ILE A 317 SHEET 6 A 6 ASP A 359 LEU A 363 1 O VAL A 360 N LEU A 342 SHEET 1 B 3 PRO A 262 PRO A 264 0 SHEET 2 B 3 GLY A 249 CYS A 256 -1 N ALA A 254 O PHE A 263 SHEET 3 B 3 VAL A 287 ILE A 291 -1 O ASP A 290 N SER A 253 LINK C ACE B 800 N ARG B 801 1555 1555 1.40 LINK C LYS B 803 N ALY B 804 1555 1555 1.58 LINK C ALY B 804 N MCM B 805 1555 1555 1.41 LINK SG CYS A 256 ZN ZN A 401 1555 1555 2.38 LINK SG CYS A 259 ZN ZN A 401 1555 1555 2.33 LINK SG CYS A 280 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 283 ZN ZN A 401 1555 1555 2.44 CISPEP 1 GLU A 325 PRO A 326 0 -2.57 SITE 1 AC1 4 CYS A 256 CYS A 259 CYS A 280 CYS A 283 CRYST1 114.809 114.809 123.202 90.00 90.00 120.00 H 3 2 18 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 0.008710 0.005029 0.000000 0.00000 SCALE2 0.000000 0.010058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008117 0.00000