PDB Short entry for 2X35 HEADER TRANSCRIPTION 21-JAN-10 2X35 TITLE MOLECULAR BASIS OF HISTONE H3K36ME3 RECOGNITION BY THE PWWP DOMAIN OF TITLE 2 BRPF1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEREGRIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BRPF1 PWWP DOMAIN, RESIDUES 1076-1205; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PRSETA KEYWDS TRANSCRIPTION, METAL-BINDING, ZINC-FINGER, DNA-BINDING, CHROMATIN KEYWDS 2 REGULATOR, TRANSCRIPTION REGULATION, NUCLEOSOME EXPDTA X-RAY DIFFRACTION AUTHOR A.VEZZOLI,N.BONADIES,M.D.ALLEN,S.M.V.FREUND,C.M.SANTIVERI,B.KVINLAUG, AUTHOR 2 B.J.P.HUNTLY,B.GOTTGENS,M.BYCROFT REVDAT 5 24-JAN-18 2X35 1 SOURCE REVDAT 4 25-MAY-11 2X35 1 JRNL REMARK DBREF SEQADV REVDAT 3 28-APR-10 2X35 1 KEYWDS JRNL REVDAT 2 21-APR-10 2X35 1 KEYWDS JRNL REVDAT 1 02-FEB-10 2X35 0 JRNL AUTH A.VEZZOLI,N.BONADIES,M.D.ALLEN,S.M.V.FREUND,C.M.SANTIVERI, JRNL AUTH 2 B.KVINLAUG,B.J.P.HUNTLY,B.GOTTGENS,M.BYCROFT JRNL TITL MOLECULAR BASIS OF HISTONE H3K36ME3 RECOGNITION BY THE PWWP JRNL TITL 2 DOMAIN OF BRPF1. JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 617 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20400950 JRNL DOI 10.1038/NSMB.1797 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 10632 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 997 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 34.4257 - 3.8244 0.96 2705 126 0.1746 0.2126 REMARK 3 2 3.8244 - 3.0361 0.98 2780 152 0.1785 0.1985 REMARK 3 3 3.0361 - 2.6525 0.98 2764 148 0.2083 0.2428 REMARK 3 4 2.6525 - 2.4100 0.96 2683 163 0.2028 0.2631 REMARK 3 5 2.4100 - 2.2373 0.94 2621 161 0.2112 0.2471 REMARK 3 6 2.2373 - 2.1054 0.92 2599 128 0.2347 0.2599 REMARK 3 7 2.1054 - 2.0000 0.88 2481 119 0.2795 0.3994 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 : 0.37 REMARK 3 B_SOL : 54.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.45820 REMARK 3 B22 (A**2) : 28.44450 REMARK 3 B33 (A**2) : -16.98630 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 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 : 0.013 1051 REMARK 3 ANGLE : 1.284 1423 REMARK 3 CHIRALITY : 0.086 151 REMARK 3 PLANARITY : 0.006 183 REMARK 3 DIHEDRAL : 15.334 406 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: DISORDERED REGIONS WERE MODELED REMARK 3 STEREOCHEMICALLY. REMARK 4 REMARK 4 2X35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1290042576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10661 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 38.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 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: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2M LITHIUM SULPHATE, REMARK 280 0.1M TRIS (PH 8.5), 10 MM NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 57.47900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.47900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 22.10700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.19950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.10700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.19950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.47900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.10700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.19950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.47900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.10700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.19950 REMARK 290 SMTRY3 8 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 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 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 1074 REMARK 465 GLY A 1075 REMARK 465 SER A 1076 REMARK 465 GLU A 1077 REMARK 465 ASP A 1078 REMARK 465 GLU A 1079 REMARK 465 GLU A 1205 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 OE2 GLU A 1140 O HOH A 2031 2.15 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 TYR A1096 148.48 -177.00 REMARK 500 HIS A1116 41.74 35.12 REMARK 500 GLN A1136 46.02 -85.57 REMARK 500 GLU A1137 -30.38 -156.76 REMARK 500 PHE A1148 32.83 -86.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D9E RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE BROMODOMAIN OF PEREGRIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE EXTRA 2 GLYCINES ARE LEFT ON THE PROTEIN AFTER REMARK 999 TEV PROTEASE CLEAVAGE DBREF 2X35 A 1076 1205 UNP P55201 BRPF1_HUMAN 1076 1205 SEQADV 2X35 GLY A 1074 UNP P55201 EXPRESSION TAG SEQADV 2X35 GLY A 1075 UNP P55201 EXPRESSION TAG SEQRES 1 A 132 GLY GLY SER GLU ASP GLU ASP SER PRO LEU ASP ALA LEU SEQRES 2 A 132 ASP LEU VAL TRP ALA LYS CYS ARG GLY TYR PRO SER TYR SEQRES 3 A 132 PRO ALA LEU ILE ILE ASP PRO LYS MET PRO ARG GLU GLY SEQRES 4 A 132 MET PHE HIS HIS GLY VAL PRO ILE PRO VAL PRO PRO LEU SEQRES 5 A 132 GLU VAL LEU LYS LEU GLY GLU GLN MET THR GLN GLU ALA SEQRES 6 A 132 ARG GLU HIS LEU TYR LEU VAL LEU PHE PHE ASP ASN LYS SEQRES 7 A 132 ARG THR TRP GLN TRP LEU PRO ARG THR LYS LEU VAL PRO SEQRES 8 A 132 LEU GLY VAL ASN GLN ASP LEU ASP LYS GLU LYS MET LEU SEQRES 9 A 132 GLU GLY ARG LYS SER ASN ILE ARG LYS SER VAL GLN ILE SEQRES 10 A 132 ALA TYR HIS ARG ALA LEU GLN HIS ARG SER LYS VAL GLN SEQRES 11 A 132 GLY GLU FORMUL 2 HOH *64(H2 O) HELIX 1 1 PRO A 1124 GLN A 1136 1 13 HELIX 2 2 ASN A 1168 LEU A 1177 1 10 HELIX 3 3 LYS A 1181 GLN A 1203 1 23 SHEET 1 AA 5 TRP A1154 PRO A1158 0 SHEET 2 AA 5 LEU A1142 PHE A1147 -1 O TYR A1143 N LEU A1157 SHEET 3 AA 5 TYR A1099 ILE A1104 -1 O LEU A1102 N LEU A1146 SHEET 4 AA 5 LEU A1088 ALA A1091 -1 O VAL A1089 N ALA A1101 SHEET 5 AA 5 LEU A1162 PRO A1164 -1 O VAL A1163 N TRP A1090 SHEET 1 AB 2 MET A1113 HIS A1115 0 SHEET 2 AB 2 VAL A1118 ILE A1120 -1 O VAL A1118 N HIS A1115 CRYST1 44.214 62.399 114.958 90.00 90.00 90.00 C 2 2 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 0.022617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008699 0.00000