HEADER TRANSCRIPTION 28-APR-22 7UU0 TITLE CRYSTAL STRUCTURE OF THE BRD2-BD2 IN COMPLEX WITH A LIGAND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 3 OF BROMODOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: O27.1.1,REALLY INTERESTING NEW GENE 3 PROTEIN; 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: BRD2, KIAA9001, RING3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BPTF, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR P.KALRA,K.SHI,H.AIHARA,W.C.K.POMERANTZ REVDAT 1 03-MAY-23 7UU0 0 JRNL AUTH P.KALRA,K.SHI,H.AIHARA,W.C.K.POMERANTZ JRNL TITL CRYSTAL STRUCTURE OF THE BRD2-BD2 IN COMPLEX WITH A LIGAND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 30337 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 1435 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 42.2700 - 2.8000 0.96 2996 149 0.1519 0.1572 REMARK 3 2 2.8000 - 2.2200 0.99 2953 135 0.1428 0.1810 REMARK 3 3 2.2200 - 1.9400 0.98 2887 144 0.1341 0.1493 REMARK 3 4 1.9400 - 1.7600 1.00 2913 144 0.1371 0.1810 REMARK 3 5 1.7600 - 1.6400 1.00 2891 140 0.1197 0.1549 REMARK 3 6 1.6400 - 1.5400 1.00 2861 157 0.1124 0.1604 REMARK 3 7 1.5400 - 1.4600 0.99 2851 142 0.1239 0.1833 REMARK 3 8 1.4600 - 1.4000 1.00 2881 136 0.1413 0.2141 REMARK 3 9 1.4000 - 1.3500 1.00 2843 147 0.1513 0.2204 REMARK 3 10 1.3500 - 1.3000 0.98 2826 141 0.1602 0.2249 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.64 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7UU0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000264602. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30368 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 52.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE 20% POLYETHYLENE REMARK 280 GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.26300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.60800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.26300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.60800 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 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 759 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 768 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 842 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 MET A 321 REMARK 465 HIS A 322 REMARK 465 HIS A 323 REMARK 465 HIS A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 SER A 328 REMARK 465 SER A 329 REMARK 465 GLY A 330 REMARK 465 VAL A 331 REMARK 465 ASP A 332 REMARK 465 LEU A 333 REMARK 465 GLY A 334 REMARK 465 THR A 335 REMARK 465 GLU A 336 REMARK 465 ASN A 337 REMARK 465 LEU A 338 REMARK 465 TYR A 339 REMARK 465 PHE A 340 REMARK 465 GLN A 341 REMARK 465 ASP A 455 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 683 O HOH A 821 2.06 REMARK 500 O HOH A 608 O HOH A 687 2.18 REMARK 500 O HOH A 681 O HOH A 761 2.18 REMARK 500 O HOH A 608 O HOH A 707 2.19 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 840 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 841 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 842 DISTANCE = 6.54 ANGSTROMS DBREF 7UU0 A 344 455 UNP P25440 BRD2_HUMAN 297 408 SEQADV 7UU0 MET A 321 UNP P25440 EXPRESSION TAG SEQADV 7UU0 HIS A 322 UNP P25440 EXPRESSION TAG SEQADV 7UU0 HIS A 323 UNP P25440 EXPRESSION TAG SEQADV 7UU0 HIS A 324 UNP P25440 EXPRESSION TAG SEQADV 7UU0 HIS A 325 UNP P25440 EXPRESSION TAG SEQADV 7UU0 HIS A 326 UNP P25440 EXPRESSION TAG SEQADV 7UU0 HIS A 327 UNP P25440 EXPRESSION TAG SEQADV 7UU0 SER A 328 UNP P25440 EXPRESSION TAG SEQADV 7UU0 SER A 329 UNP P25440 EXPRESSION TAG SEQADV 7UU0 GLY A 330 UNP P25440 EXPRESSION TAG SEQADV 7UU0 VAL A 331 UNP P25440 EXPRESSION TAG SEQADV 7UU0 ASP A 332 UNP P25440 EXPRESSION TAG SEQADV 7UU0 LEU A 333 UNP P25440 EXPRESSION TAG SEQADV 7UU0 GLY A 334 UNP P25440 EXPRESSION TAG SEQADV 7UU0 THR A 335 UNP P25440 EXPRESSION TAG SEQADV 7UU0 GLU A 336 UNP P25440 EXPRESSION TAG SEQADV 7UU0 ASN A 337 UNP P25440 EXPRESSION TAG SEQADV 7UU0 LEU A 338 UNP P25440 EXPRESSION TAG SEQADV 7UU0 TYR A 339 UNP P25440 EXPRESSION TAG SEQADV 7UU0 PHE A 340 UNP P25440 EXPRESSION TAG SEQADV 7UU0 GLN A 341 UNP P25440 EXPRESSION TAG SEQADV 7UU0 SER A 342 UNP P25440 EXPRESSION TAG SEQADV 7UU0 MET A 343 UNP P25440 EXPRESSION TAG SEQRES 1 A 135 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 135 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLY LYS LEU SEQRES 3 A 135 SER GLU GLN LEU LYS HIS CYS ASN GLY ILE LEU LYS GLU SEQRES 4 A 135 LEU LEU SER LYS LYS HIS ALA ALA TYR ALA TRP PRO PHE SEQRES 5 A 135 TYR LYS PRO VAL ASP ALA SER ALA LEU GLY LEU HIS ASP SEQRES 6 A 135 TYR HIS ASP ILE ILE LYS HIS PRO MET ASP LEU SER THR SEQRES 7 A 135 VAL LYS ARG LYS MET GLU ASN ARG ASP TYR ARG ASP ALA SEQRES 8 A 135 GLN GLU PHE ALA ALA ASP VAL ARG LEU MET PHE SER ASN SEQRES 9 A 135 CYS TYR LYS TYR ASN PRO PRO ASP HIS ASP VAL VAL ALA SEQRES 10 A 135 MET ALA ARG LYS LEU GLN ASP VAL PHE GLU PHE ARG TYR SEQRES 11 A 135 ALA LYS MET PRO ASP HET EDO A 501 4 HET QJ1 A 502 16 HETNAM EDO 1,2-ETHANEDIOL HETNAM QJ1 METHYL (7S)-7-(THIOPHEN-2-YL)-1,4-THIAZEPANE-4- HETNAM 2 QJ1 CARBOXYLATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 QJ1 C11 H15 N O2 S2 FORMUL 4 HOH *242(H2 O) HELIX 1 AA1 SER A 347 SER A 362 1 16 HELIX 2 AA2 HIS A 365 TRP A 370 1 6 HELIX 3 AA3 PRO A 371 TYR A 373 5 3 HELIX 4 AA4 ASP A 377 GLY A 382 1 6 HELIX 5 AA5 ASP A 385 ILE A 390 1 6 HELIX 6 AA6 ASP A 395 ASN A 405 1 11 HELIX 7 AA7 ASP A 410 ASN A 429 1 20 HELIX 8 AA8 HIS A 433 ALA A 451 1 19 CRYST1 32.309 52.526 71.216 90.00 90.00 90.00 P 2 21 21 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 0.030951 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014042 0.00000