HEADER TRANSCRIPTION 21-NOV-16 5MGL TITLE CRYSTAL STRUCTURE OF BAZ2A BROMODOMAIN IN COMPLEX WITH 4- TITLE 2 CHLOROPYRIDINE DERIVATIVE 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BROMODOMAIN, UNP RESIDUES 1796-1898; COMPND 5 SYNONYM: TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5, COMPND 6 TIP5,HWALP3; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: FIRST TWO RESIDUES SM DERIVE FROM THE EXPRESSION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: BAZ2A, KIAA0314, TIP5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FOUR HELICAL BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.LOLLI,D.SPILIOTOPOULOS,A.CAFLISCH REVDAT 3 17-JAN-24 5MGL 1 REMARK REVDAT 2 06-SEP-17 5MGL 1 JRNL REVDAT 1 12-APR-17 5MGL 0 JRNL AUTH D.SPILIOTOPOULOS,E.C.WAMHOFF,G.LOLLI,C.RADEMACHER,A.CAFLISCH JRNL TITL DISCOVERY OF BAZ2A BROMODOMAIN LIGANDS. JRNL REF EUR J MED CHEM V. 139 564 2017 JRNL REFN ISSN 1768-3254 JRNL PMID 28837921 JRNL DOI 10.1016/J.EJMECH.2017.08.028 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 5172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.320 REMARK 3 FREE R VALUE TEST SET COUNT : 275 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 27.0645 - 3.3386 1.00 2498 125 0.1883 0.2353 REMARK 3 2 3.3386 - 2.6507 1.00 2399 150 0.2587 0.2772 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.18 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 : 0.002 867 REMARK 3 ANGLE : 0.611 1168 REMARK 3 CHIRALITY : 0.021 117 REMARK 3 PLANARITY : 0.004 154 REMARK 3 DIHEDRAL : 12.755 322 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1799 THROUGH 1810 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.1671 22.5746 7.2298 REMARK 3 T TENSOR REMARK 3 T11: 0.1566 T22: 0.2052 REMARK 3 T33: 0.3286 T12: -0.0777 REMARK 3 T13: 0.0866 T23: 0.0426 REMARK 3 L TENSOR REMARK 3 L11: 0.0879 L22: 0.0119 REMARK 3 L33: 0.0458 L12: -0.0100 REMARK 3 L13: 0.0391 L23: 0.0076 REMARK 3 S TENSOR REMARK 3 S11: -0.0895 S12: 0.0364 S13: -0.0271 REMARK 3 S21: -0.0086 S22: -0.0363 S23: -0.0629 REMARK 3 S31: 0.1198 S32: -0.0300 S33: -0.1113 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1811 THROUGH 1839 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.2700 36.7737 -6.4937 REMARK 3 T TENSOR REMARK 3 T11: 0.2047 T22: 0.4271 REMARK 3 T33: 0.2561 T12: -0.0501 REMARK 3 T13: 0.0216 T23: -0.0362 REMARK 3 L TENSOR REMARK 3 L11: 0.0295 L22: 0.2662 REMARK 3 L33: 0.0634 L12: -0.0489 REMARK 3 L13: -0.0108 L23: 0.1276 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: 0.1044 S13: -0.1313 REMARK 3 S21: -0.1695 S22: 0.1152 S23: 0.0373 REMARK 3 S31: -0.1154 S32: -0.2603 S33: -0.0007 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1840 THROUGH 1872 ) REMARK 3 ORIGIN FOR THE GROUP (A): 65.5570 26.1121 -2.4726 REMARK 3 T TENSOR REMARK 3 T11: 0.1818 T22: 0.1930 REMARK 3 T33: 0.2191 T12: -0.0755 REMARK 3 T13: 0.1417 T23: -0.0813 REMARK 3 L TENSOR REMARK 3 L11: 0.3441 L22: 0.4436 REMARK 3 L33: 0.5459 L12: 0.1827 REMARK 3 L13: 0.1904 L23: -0.2153 REMARK 3 S TENSOR REMARK 3 S11: -0.2292 S12: 0.2039 S13: -0.2016 REMARK 3 S21: -0.0910 S22: -0.0609 S23: -0.2460 REMARK 3 S31: -0.0171 S32: 0.0015 S33: -0.3772 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1873 THROUGH 1898 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.5308 35.0834 7.0285 REMARK 3 T TENSOR REMARK 3 T11: 0.0443 T22: 0.2255 REMARK 3 T33: 0.0857 T12: -0.0341 REMARK 3 T13: -0.0010 T23: 0.0109 REMARK 3 L TENSOR REMARK 3 L11: 0.1239 L22: 0.5256 REMARK 3 L33: 0.2256 L12: 0.1173 REMARK 3 L13: 0.0328 L23: 0.0829 REMARK 3 S TENSOR REMARK 3 S11: 0.0968 S12: -0.3111 S13: 0.0586 REMARK 3 S21: 0.2520 S22: 0.0679 S23: -0.0113 REMARK 3 S31: 0.0202 S32: -0.0490 S33: 0.0300 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 5MGL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 27.063 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.26800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.93600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4LZ2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M MGCL2, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 10.94667 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 21.89333 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 21.89333 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 10.94667 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: 6070 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 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 1794 REMARK 465 MET A 1795 REMARK 465 HIS A 1796 REMARK 465 SER A 1797 REMARK 465 ASP A 1798 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 A2051 DISTANCE = 6.16 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7MU A 1901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5MGG RELATED DB: PDB REMARK 900 5MGG CONTAINS THE SAME LIGAND COMPLEXED WITH A DIFFERENT REMARK 900 BROMODOMAIN (BAZ2B). REMARK 900 RELATED ID: 5MGJ RELATED DB: PDB REMARK 900 5MGJ CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT. REMARK 900 RELATED ID: 5MGK RELATED DB: PDB REMARK 900 5MGK CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT. DBREF 5MGL A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 5MGL SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 5MGL MET A 1795 UNP Q9UIF9 EXPRESSION TAG SEQRES 1 A 105 SER MET HIS SER ASP LEU THR PHE CYS GLU ILE ILE LEU SEQRES 2 A 105 MET GLU MET GLU SER HIS ASP ALA ALA TRP PRO PHE LEU SEQRES 3 A 105 GLU PRO VAL ASN PRO ARG LEU VAL SER GLY TYR ARG ARG SEQRES 4 A 105 ILE ILE LYS ASN PRO MET ASP PHE SER THR MET ARG GLU SEQRES 5 A 105 ARG LEU LEU ARG GLY GLY TYR THR SER SER GLU GLU PHE SEQRES 6 A 105 ALA ALA ASP ALA LEU LEU VAL PHE ASP ASN CYS GLN THR SEQRES 7 A 105 PHE ASN GLU ASP ASP SER GLU VAL GLY LYS ALA GLY HIS SEQRES 8 A 105 ILE MET ARG ARG PHE PHE GLU SER ARG TRP GLU GLU PHE SEQRES 9 A 105 TYR HET 7MU A1901 11 HETNAM 7MU 4-CHLORANYL-~{N}-METHYL-PYRIDINE-2-CARBOXAMIDE FORMUL 2 7MU C7 H7 CL N2 O FORMUL 3 HOH *51(H2 O) HELIX 1 AA1 LEU A 1799 SER A 1811 1 13 HELIX 2 AA2 HIS A 1812 TRP A 1816 5 5 HELIX 3 AA3 GLY A 1829 ILE A 1834 1 6 HELIX 4 AA4 ASP A 1839 GLY A 1850 1 12 HELIX 5 AA5 SER A 1854 ASN A 1873 1 20 HELIX 6 AA6 SER A 1877 TYR A 1898 1 22 SITE 1 AC1 7 PRO A1817 PHE A1818 VAL A1822 TYR A1830 SITE 2 AC1 7 PHE A1872 ASN A1873 HOH A2003 CRYST1 95.550 95.550 32.840 90.00 90.00 120.00 P 31 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 0.010466 0.006042 0.000000 0.00000 SCALE2 0.000000 0.012085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030450 0.00000