HEADER DNA BINDING PROTEIN 02-OCT-15 5E3D
TITLE CRYSTAL STRUCTURE OF THE HUMAN BRPF1 BROMODOMAIN IN COMPLEX WITH SEED7
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PEREGRIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 626-740;
COMPND 5 SYNONYM: BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1,PROTEIN
COMPND 6 BR140;
COMPND 7 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: BRPF1, BR140;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1(BRPF1), MONOCYTIC
KEYWDS 2 LEUKEMIA ZINC-FINGER (MOZ), INHIBITOR, TRANSCRIPTION, DNA BINDING
KEYWDS 3 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR J.ZHU,A.CAFLISCH
REVDAT 3 10-JAN-24 5E3D 1 REMARK
REVDAT 2 22-JUN-16 5E3D 1 JRNL
REVDAT 1 25-MAY-16 5E3D 0
JRNL AUTH J.ZHU,A.CAFLISCH
JRNL TITL TWENTY CRYSTAL STRUCTURES OF BROMODOMAIN AND PHD FINGER
JRNL TITL 2 CONTAINING PROTEIN 1 (BRPF1)/LIGAND COMPLEXES REVEAL
JRNL TITL 3 CONSERVED BINDING MOTIFS AND RARE INTERACTIONS.
JRNL REF J.MED.CHEM. V. 59 5555 2016
JRNL REFN ISSN 0022-2623
JRNL PMID 27167503
JRNL DOI 10.1021/ACS.JMEDCHEM.6B00215
REMARK 2
REMARK 2 RESOLUTION. 1.71 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.10_2155: ???)
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) : 1.71
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.22
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 14776
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.194
REMARK 3 R VALUE (WORKING SET) : 0.193
REMARK 3 FREE R VALUE : 0.222
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010
REMARK 3 FREE R VALUE TEST SET COUNT : 740
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 40.2340 - 2.9210 0.99 2912 154 0.1746 0.1853
REMARK 3 2 2.9210 - 2.3185 1.00 2829 149 0.2247 0.2969
REMARK 3 3 2.3185 - 2.0254 1.00 2770 146 0.1966 0.2366
REMARK 3 4 2.0254 - 1.8403 1.00 2780 147 0.2182 0.2613
REMARK 3 5 1.8403 - 1.7100 0.99 2745 144 0.2410 0.3194
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) : 0.180
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.160
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 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 : 0.007 977
REMARK 3 ANGLE : 0.710 1322
REMARK 3 CHIRALITY : 0.043 141
REMARK 3 PLANARITY : 0.005 174
REMARK 3 DIHEDRAL : 14.934 598
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): 14.8064 -22.5434 0.5016
REMARK 3 T TENSOR
REMARK 3 T11: 0.3209 T22: 0.3044
REMARK 3 T33: 0.3046 T12: -0.1339
REMARK 3 T13: -0.0532 T23: 0.0460
REMARK 3 L TENSOR
REMARK 3 L11: 3.2971 L22: 6.3754
REMARK 3 L33: 2.4937 L12: -1.0939
REMARK 3 L13: 0.8432 L23: -1.6162
REMARK 3 S TENSOR
REMARK 3 S11: 0.0624 S12: -0.4228 S13: -0.2708
REMARK 3 S21: 0.6974 S22: -0.2497 S23: -0.1323
REMARK 3 S31: -0.1560 S32: 0.0309 S33: 0.1570
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 5E3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-15.
REMARK 100 THE DEPOSITION ID IS D_1000214281.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JUL-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.99987
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14799
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710
REMARK 200 RESOLUTION RANGE LOW (A) : 40.220
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 9.500
REMARK 200 R MERGE (I) : 0.03100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1
REMARK 200 DATA REDUNDANCY IN SHELL : 9.60
REMARK 200 R MERGE FOR SHELL (I) : 0.40500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100
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: 4LC2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.27
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH5.5, 0.15 M
REMARK 280 SODIUM NITRATE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-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 41.62000
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 20.81000
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 20.81000
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 41.62000
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: 140 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 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 A 948 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 SER A 625
REMARK 465 MET A 626
REMARK 465 GLU A 627
REMARK 465 GLY A 740
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 670 CD CE NZ
REMARK 470 LYS A 706 NZ
REMARK 470 GLN A 731 CD OE1 NE2
REMARK 470 LYS A 738 CE NZ
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5JL A 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 802
DBREF 5E3D A 626 740 UNP P55201 BRPF1_HUMAN 626 740
SEQADV 5E3D SER A 625 UNP P55201 EXPRESSION TAG
SEQRES 1 A 116 SER MET GLU MET GLN LEU THR PRO PHE LEU ILE LEU LEU
SEQRES 2 A 116 ARG LYS THR LEU GLU GLN LEU GLN GLU LYS ASP THR GLY
SEQRES 3 A 116 ASN ILE PHE SER GLU PRO VAL PRO LEU SER GLU VAL PRO
SEQRES 4 A 116 ASP TYR LEU ASP HIS ILE LYS LYS PRO MET ASP PHE PHE
SEQRES 5 A 116 THR MET LYS GLN ASN LEU GLU ALA TYR ARG TYR LEU ASN
SEQRES 6 A 116 PHE ASP ASP PHE GLU GLU ASP PHE ASN LEU ILE VAL SER
SEQRES 7 A 116 ASN CYS LEU LYS TYR ASN ALA LYS ASP THR ILE PHE TYR
SEQRES 8 A 116 ARG ALA ALA VAL ARG LEU ARG GLU GLN GLY GLY ALA VAL
SEQRES 9 A 116 LEU ARG GLN ALA ARG ARG GLN ALA GLU LYS MET GLY
HET 5JL A 801 12
HET NO3 A 802 4
HETNAM 5JL 2,8-DITHIOXO-1,2,3,7,8,9-HEXAHYDRO-6H-PURIN-6-ONE
HETNAM NO3 NITRATE ION
FORMUL 2 5JL C5 H4 N4 O S2
FORMUL 3 NO3 N O3 1-
FORMUL 4 HOH *75(H2 O)
HELIX 1 AA1 GLN A 629 ASP A 648 1 20
HELIX 2 AA2 ASP A 664 HIS A 668 5 5
HELIX 3 AA3 ASP A 674 ALA A 684 1 11
HELIX 4 AA4 ASN A 689 ASN A 708 1 20
HELIX 5 AA5 THR A 712 MET A 739 1 28
SITE 1 AC1 6 ILE A 652 VAL A 657 VAL A 662 ASN A 708
SITE 2 AC1 6 PHE A 714 HOH A 907
SITE 1 AC2 7 SER A 702 LEU A 705 LYS A 706 TYR A 715
SITE 2 AC2 7 VAL A 719 ARG A 722 HOH A 910
CRYST1 60.730 60.730 62.430 90.00 90.00 120.00 P 32 2 1 6
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 0.016466 0.009507 0.000000 0.00000
SCALE2 0.000000 0.019014 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016018 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
