HEADER TRANSCRIPTION 01-MAR-16 5II2 TITLE CRYSTAL STRUCTURE OF THE FIFTH BROMODOMAIN OF HUMAN POLYBROMO (PB1) IN TITLE 2 COMPLEX WITH 2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-4H-CHROMEN-4-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN POLYBROMO-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HPB1,BRG1-ASSOCIATED FACTOR 180,BAF180,POLYBROMO-1D; COMPND 5 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: PBRM1, BAF180, PB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: R3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS BROMODOMAIN, COMPLEX, SMALL MOLECULE, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 2 SGC, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR P.FILIPPAKOPOULOS,S.PICAUD,I.FELLETAR,F.VON DELFT,A.M.EDWARDS, AUTHOR 2 C.H.ARROWSMITH,C.BOUNTRA,S.KNAPP REVDAT 4 10-JAN-24 5II2 1 LINK REVDAT 3 26-OCT-16 5II2 1 JRNL REVDAT 2 12-OCT-16 5II2 1 JRNL REVDAT 1 29-JUN-16 5II2 0 JRNL AUTH V.MYRIANTHOPOULOS,N.GABORIAUD-KOLAR,C.TALLANT,M.L.HALL, JRNL AUTH 2 S.GRIGORIOU,P.M.BROWNLEE,O.FEDOROV,C.ROGERS,D.HEIDENREICH, JRNL AUTH 3 M.WANIOR,N.DROSOS,N.MEXIA,P.SAVITSKY,T.BAGRATUNI, JRNL AUTH 4 E.KASTRITIS,E.TERPOS,P.FILIPPAKOPOULOS,S.MULLER, JRNL AUTH 5 A.L.SKALTSOUNIS,J.A.DOWNS,S.KNAPP,E.MIKROS JRNL TITL DISCOVERY AND OPTIMIZATION OF A SELECTIVE LIGAND FOR THE JRNL TITL 2 SWITCH/SUCROSE NONFERMENTING-RELATED BROMODOMAINS OF JRNL TITL 3 POLYBROMO PROTEIN-1 BY THE USE OF VIRTUAL SCREENING AND JRNL TITL 4 HYDRATION ANALYSIS. JRNL REF J.MED.CHEM. V. 59 8787 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27617704 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00355 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 19140 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1042 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1304 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1871 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.56000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -1.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.205 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1972 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1835 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2664 ; 1.623 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4214 ; 0.999 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 5.460 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;32.613 ;23.936 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;14.346 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;13.696 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 283 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2180 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 425 ; 0.001 ; 0.020 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): 911 ; 2.417 ; 3.854 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 910 ; 2.346 ; 3.850 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1135 ; 3.153 ; 7.154 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 652 A 766 REMARK 3 ORIGIN FOR THE GROUP (A): 4.6320 -5.4916 -22.5511 REMARK 3 T TENSOR REMARK 3 T11: 0.0762 T22: 0.0717 REMARK 3 T33: 0.0218 T12: 0.0066 REMARK 3 T13: 0.0070 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.2080 L22: 0.4963 REMARK 3 L33: 0.8004 L12: -0.0726 REMARK 3 L13: -0.3443 L23: 0.1440 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: 0.0049 S13: -0.0340 REMARK 3 S21: -0.0026 S22: -0.0291 S23: 0.0098 REMARK 3 S31: -0.1370 S32: -0.0388 S33: -0.0044 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 652 B 764 REMARK 3 ORIGIN FOR THE GROUP (A): 15.5826 -28.2683 -20.3152 REMARK 3 T TENSOR REMARK 3 T11: 0.0722 T22: 0.0690 REMARK 3 T33: 0.0153 T12: -0.0024 REMARK 3 T13: -0.0154 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.1308 L22: 0.4027 REMARK 3 L33: 0.7821 L12: -0.0172 REMARK 3 L13: 0.2751 L23: 0.2171 REMARK 3 S TENSOR REMARK 3 S11: 0.0206 S12: 0.0066 S13: 0.0110 REMARK 3 S21: 0.0281 S22: -0.0179 S23: -0.0001 REMARK 3 S31: 0.1077 S32: 0.0173 S33: -0.0027 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5II2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218881. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.52 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20237 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 24.186 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : 0.12700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: ENSEMBLE OF REMARK 200 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.20M K3(CIT) 0.1M BTPROP PH 7.5 20.0% REMARK 280 PEG 3350 10.0% ETGLY, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K 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 20.76000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.11500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.11500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.76000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.25500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A 643 REMARK 465 MET A 644 REMARK 465 SER A 645 REMARK 465 GLY A 646 REMARK 465 ILE A 647 REMARK 465 SER A 648 REMARK 465 PRO A 649 REMARK 465 LYS A 650 REMARK 465 LYS A 651 REMARK 465 SER B 643 REMARK 465 MET B 644 REMARK 465 SER B 645 REMARK 465 GLY B 646 REMARK 465 ILE B 647 REMARK 465 SER B 648 REMARK 465 PRO B 649 REMARK 465 LYS B 650 REMARK 465 LYS B 651 REMARK 465 GLY B 765 REMARK 465 ASP B 766 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 675 CD CE NZ REMARK 470 LYS A 701 CG CD CE NZ REMARK 470 GLN A 719 CG CD OE1 NE2 REMARK 470 LYS A 754 CE NZ REMARK 470 LYS B 661 CD CE NZ REMARK 470 LYS B 701 CG CD CE NZ REMARK 470 LYS B 708 CE NZ REMARK 470 LYS B 717 CE NZ REMARK 470 LYS B 754 O REMARK 470 ARG B 761 CD NE CZ NH1 NH2 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 A 678 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 678 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 678 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP B 748 CB - CG - OD1 ANGL. DEV. = 5.5 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 ASP A 695 -7.34 78.56 REMARK 500 ASN A 716 39.47 70.88 REMARK 500 LEU B 763 32.04 -99.48 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 K A 801 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 736 O REMARK 620 2 THR A 737 O 71.2 REMARK 620 3 ASN A 739 O 69.1 89.5 REMARK 620 4 HOH A 934 O 127.5 67.8 79.1 REMARK 620 5 HOH A 977 O 97.2 70.4 158.9 98.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 801 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CIT A 802 O1 REMARK 620 2 CIT A 802 O5 69.3 REMARK 620 3 HOH A 949 O 90.4 37.5 REMARK 620 4 HOH A 971 O 90.5 34.1 4.3 REMARK 620 5 CYS B 736 O 85.5 38.1 6.3 9.6 REMARK 620 6 THR B 737 O 85.1 33.9 5.4 6.5 4.6 REMARK 620 7 ASN B 739 O 86.8 34.8 3.7 5.1 4.8 1.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LU2 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LU2 B 802 DBREF 5II2 A 645 766 UNP Q86U86 PB1_HUMAN 645 766 DBREF 5II2 B 645 766 UNP Q86U86 PB1_HUMAN 645 766 SEQADV 5II2 SER A 643 UNP Q86U86 EXPRESSION TAG SEQADV 5II2 MET A 644 UNP Q86U86 EXPRESSION TAG SEQADV 5II2 SER B 643 UNP Q86U86 EXPRESSION TAG SEQADV 5II2 MET B 644 UNP Q86U86 EXPRESSION TAG SEQRES 1 A 124 SER MET SER GLY ILE SER PRO LYS LYS SER LYS TYR MET SEQRES 2 A 124 THR PRO MET GLN GLN LYS LEU ASN GLU VAL TYR GLU ALA SEQRES 3 A 124 VAL LYS ASN TYR THR ASP LYS ARG GLY ARG ARG LEU SER SEQRES 4 A 124 ALA ILE PHE LEU ARG LEU PRO SER ARG SER GLU LEU PRO SEQRES 5 A 124 ASP TYR TYR LEU THR ILE LYS LYS PRO MET ASP MET GLU SEQRES 6 A 124 LYS ILE ARG SER HIS MET MET ALA ASN LYS TYR GLN ASP SEQRES 7 A 124 ILE ASP SER MET VAL GLU ASP PHE VAL MET MET PHE ASN SEQRES 8 A 124 ASN ALA CYS THR TYR ASN GLU PRO GLU SER LEU ILE TYR SEQRES 9 A 124 LYS ASP ALA LEU VAL LEU HIS LYS VAL LEU LEU GLU THR SEQRES 10 A 124 ARG ARG ASP LEU GLU GLY ASP SEQRES 1 B 124 SER MET SER GLY ILE SER PRO LYS LYS SER LYS TYR MET SEQRES 2 B 124 THR PRO MET GLN GLN LYS LEU ASN GLU VAL TYR GLU ALA SEQRES 3 B 124 VAL LYS ASN TYR THR ASP LYS ARG GLY ARG ARG LEU SER SEQRES 4 B 124 ALA ILE PHE LEU ARG LEU PRO SER ARG SER GLU LEU PRO SEQRES 5 B 124 ASP TYR TYR LEU THR ILE LYS LYS PRO MET ASP MET GLU SEQRES 6 B 124 LYS ILE ARG SER HIS MET MET ALA ASN LYS TYR GLN ASP SEQRES 7 B 124 ILE ASP SER MET VAL GLU ASP PHE VAL MET MET PHE ASN SEQRES 8 B 124 ASN ALA CYS THR TYR ASN GLU PRO GLU SER LEU ILE TYR SEQRES 9 B 124 LYS ASP ALA LEU VAL LEU HIS LYS VAL LEU LEU GLU THR SEQRES 10 B 124 ARG ARG ASP LEU GLU GLY ASP HET K A 801 1 HET CIT A 802 13 HET LU2 A 803 21 HET K B 801 1 HET LU2 B 802 21 HETNAM K POTASSIUM ION HETNAM CIT CITRIC ACID HETNAM LU2 2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-4H-CHROMEN-4-ONE HETSYN LU2 LUTEOLIN FORMUL 3 K 2(K 1+) FORMUL 4 CIT C6 H8 O7 FORMUL 5 LU2 2(C15 H10 O6) FORMUL 8 HOH *182(H2 O) HELIX 1 AA1 THR A 656 TYR A 672 1 17 HELIX 2 AA2 SER A 681 LEU A 685 5 5 HELIX 3 AA3 ASP A 695 ILE A 700 1 6 HELIX 4 AA4 ASP A 705 ALA A 715 1 11 HELIX 5 AA5 ASP A 720 ASN A 739 1 20 HELIX 6 AA6 SER A 743 LEU A 763 1 21 HELIX 7 AA7 THR B 656 TYR B 672 1 17 HELIX 8 AA8 ARG B 679 LEU B 685 5 7 HELIX 9 AA9 ASP B 695 ILE B 700 1 6 HELIX 10 AB1 ASP B 705 ALA B 715 1 11 HELIX 11 AB2 ASP B 720 ASN B 739 1 20 HELIX 12 AB3 SER B 743 LEU B 763 1 21 LINK O CYS A 736 K K A 801 1555 1555 2.83 LINK O THR A 737 K K A 801 1555 1555 2.95 LINK O ASN A 739 K K A 801 1555 1555 2.69 LINK K K A 801 O HOH A 934 1555 1555 3.08 LINK K K A 801 O HOH A 977 1555 1555 2.82 LINK O1 CIT A 802 K K B 801 1555 3654 2.61 LINK O5 CIT A 802 K K B 801 1555 3654 2.94 LINK O HOH A 949 K K B 801 3644 1555 2.77 LINK O HOH A 971 K K B 801 3644 1555 2.68 LINK O CYS B 736 K K B 801 1555 1555 2.74 LINK O THR B 737 K K B 801 1555 1555 2.78 LINK O ASN B 739 K K B 801 1555 1555 2.65 SITE 1 AC1 5 CYS A 736 THR A 737 ASN A 739 HOH A 934 SITE 2 AC1 5 HOH A 977 SITE 1 AC2 14 ARG A 690 TYR A 697 HOH A 902 HOH A 916 SITE 2 AC2 14 HOH A 921 HOH A 925 HOH A 935 HOH A 945 SITE 3 AC2 14 HOH A 949 ARG B 676 CYS B 736 PRO B 741 SITE 4 AC2 14 TYR B 746 K B 801 SITE 1 AC3 16 ILE A 683 PHE A 684 LEU A 687 PRO A 688 SITE 2 AC3 16 TYR A 696 MET A 704 ASP A 705 MET A 731 SITE 3 AC3 16 ALA A 735 ASN A 739 ILE A 745 HOH A 910 SITE 4 AC3 16 HOH A 952 HOH A 962 LEU B 744 ILE B 745 SITE 1 AC4 6 CIT A 802 HOH A 949 HOH A 971 CYS B 736 SITE 2 AC4 6 THR B 737 ASN B 739 SITE 1 AC5 14 ILE A 683 LEU A 744 ILE B 683 PHE B 684 SITE 2 AC5 14 LEU B 687 PRO B 688 TYR B 696 MET B 704 SITE 3 AC5 14 ASP B 705 MET B 731 ALA B 735 ASN B 739 SITE 4 AC5 14 HOH B 904 HOH B 951 CRYST1 41.520 58.510 138.230 90.00 90.00 90.00 P 21 21 21 8 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 0.024085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007234 0.00000