HEADER TRANSCRIPTION 23-MAY-17 5O38 TITLE HUMAN BRD2(BD2) MUTANT IN FREE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS THE BROMODOMAIN AND EXTRA-TERMINAL DOMAIN (BET) FAMILY CHROMATIN KEYWDS 2 BINDING PROTEIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.-H.CHAN,A.C.RUNCIE,A.CIULLI REVDAT 3 17-JAN-24 5O38 1 REMARK REVDAT 2 16-MAY-18 5O38 1 JRNL REVDAT 1 14-FEB-18 5O38 0 JRNL AUTH A.C.RUNCIE,M.ZENGERLE,K.H.CHAN,A.TESTA,L.VAN BEURDEN, JRNL AUTH 2 M.G.J.BAUD,O.EPEMOLU,L.C.J.ELLIS,K.D.READ,V.COULTHARD, JRNL AUTH 3 A.BRIEN,A.CIULLI JRNL TITL OPTIMIZATION OF A "BUMP-AND-HOLE" APPROACH TO JRNL TITL 2 ALLELE-SELECTIVE BET BROMODOMAIN INHIBITION. JRNL REF CHEM SCI V. 9 2452 2018 JRNL REFN ISSN 2041-6520 JRNL PMID 29732121 JRNL DOI 10.1039/C7SC02536J REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 37657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.119 REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1833 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 19.5012 - 2.8190 0.98 2915 180 0.1411 0.1720 REMARK 3 2 2.8190 - 2.2386 1.00 2852 140 0.1394 0.1366 REMARK 3 3 2.2386 - 1.9559 0.98 2767 143 0.1168 0.1133 REMARK 3 4 1.9559 - 1.7772 0.99 2804 130 0.1143 0.1446 REMARK 3 5 1.7772 - 1.6499 1.00 2771 158 0.1041 0.1279 REMARK 3 6 1.6499 - 1.5527 1.00 2795 132 0.0933 0.1222 REMARK 3 7 1.5527 - 1.4749 0.99 2739 134 0.0921 0.1273 REMARK 3 8 1.4749 - 1.4108 0.99 2789 118 0.0965 0.1320 REMARK 3 9 1.4108 - 1.3565 0.99 2772 139 0.0971 0.1399 REMARK 3 10 1.3565 - 1.3097 0.99 2730 125 0.0980 0.1394 REMARK 3 11 1.3097 - 1.2687 0.98 2693 152 0.0982 0.1475 REMARK 3 12 1.2687 - 1.2325 0.97 2646 152 0.0986 0.1383 REMARK 3 13 1.2325 - 1.2000 0.92 2551 130 0.1081 0.1298 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.140 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 : 0.005 1055 REMARK 3 ANGLE : 1.030 1429 REMARK 3 CHIRALITY : 0.076 146 REMARK 3 PLANARITY : 0.005 182 REMARK 3 DIHEDRAL : 10.751 427 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: NULL REMARK 4 REMARK 4 5O38 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200005030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9174 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37657 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 19.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02237 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.08386 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.620 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4QEU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH8.0 50% PENTAERYTHRITOL REMARK 280 PROPOXYLATE (5/4 PO/OH) 0.2M IMIDAZOLE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 26.21000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.70450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.21000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.70450 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 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 CL CL A 502 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 836 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 342 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 O HOH A 710 O HOH A 801 2.08 REMARK 500 O HOH A 635 O HOH A 808 2.15 REMARK 500 NZ LYS A 427 O HOH A 601 2.17 REMARK 500 O HOH A 612 O HOH A 785 2.17 REMARK 500 NH1 ARG A 440 O HOH A 602 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 834 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 835 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 836 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 837 DISTANCE = 6.69 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JB A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DQW A 503 DBREF 5O38 A 344 455 UNP P25440 BRD2_HUMAN 344 455 SEQADV 5O38 SER A 342 UNP P25440 EXPRESSION TAG SEQADV 5O38 MET A 343 UNP P25440 EXPRESSION TAG SEQADV 5O38 VAL A 383 UNP P25440 LEU 383 ENGINEERED MUTATION SEQRES 1 A 114 SER MET GLY LYS LEU SER GLU GLN LEU LYS HIS CYS ASN SEQRES 2 A 114 GLY ILE LEU LYS GLU LEU LEU SER LYS LYS HIS ALA ALA SEQRES 3 A 114 TYR ALA TRP PRO PHE TYR LYS PRO VAL ASP ALA SER ALA SEQRES 4 A 114 LEU GLY VAL HIS ASP TYR HIS ASP ILE ILE LYS HIS PRO SEQRES 5 A 114 MET ASP LEU SER THR VAL LYS ARG LYS MET GLU ASN ARG SEQRES 6 A 114 ASP TYR ARG ASP ALA GLN GLU PHE ALA ALA ASP VAL ARG SEQRES 7 A 114 LEU MET PHE SER ASN CYS TYR LYS TYR ASN PRO PRO ASP SEQRES 8 A 114 HIS ASP VAL VAL ALA MET ALA ARG LYS LEU GLN ASP VAL SEQRES 9 A 114 PHE GLU PHE ARG TYR ALA LYS MET PRO ASP HET 9JB A 501 51 HET CL A 502 1 HET DQW A 503 23 HETNAM 9JB 3-[(2~{R})-2-OXIDANYLPROPOXY]-2-[[(2~{R})-2- HETNAM 2 9JB OXIDANYLPROPOXY]METHYL]-2-[[(2~{S})-2- HETNAM 3 9JB OXIDANYLPROPOXY]METHYL]PROPAN-1-OL HETNAM CL CHLORIDE ION HETNAM DQW (2~{S})-1-[(2~{S})-2-OXIDANYLPROPOXY]PROPAN-2-OL FORMUL 2 9JB C14 H30 O7 FORMUL 3 CL CL 1- FORMUL 4 DQW C6 H14 O3 FORMUL 5 HOH *237(H2 O) HELIX 1 AA1 SER A 347 LEU A 361 1 15 HELIX 2 AA2 SER A 362 LYS A 364 5 3 HELIX 3 AA3 HIS A 365 TRP A 370 1 6 HELIX 4 AA4 PRO A 371 TYR A 373 5 3 HELIX 5 AA5 ASP A 377 GLY A 382 1 6 HELIX 6 AA6 ASP A 385 ILE A 390 1 6 HELIX 7 AA7 ASP A 395 ASN A 405 1 11 HELIX 8 AA8 ASP A 410 ASN A 429 1 20 HELIX 9 AA9 HIS A 433 ALA A 451 1 19 SITE 1 AC1 8 TRP A 370 PRO A 371 PHE A 372 ASN A 429 SITE 2 AC1 8 VAL A 435 HOH A 620 HOH A 698 HOH A 830 SITE 1 AC2 2 ARG A 419 HOH A 657 SITE 1 AC3 6 TYR A 426 ARG A 440 GLN A 443 ASP A 444 SITE 2 AC3 6 GLU A 447 HOH A 618 CRYST1 52.420 71.409 31.969 90.00 90.00 90.00 P 21 21 2 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 0.019077 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031280 0.00000