PDB Short entry for 5MGJ HEADER TRANSCRIPTION 21-NOV-16 5MGJ TITLE CRYSTAL STRUCTURE OF BAZ2A BROMODOMAIN IN COMPLEX WITH 1- TITLE 2 METHYLPYRIDINE DERIVATIVE 1 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 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 5MGJ 1 REMARK REVDAT 2 06-SEP-17 5MGJ 1 JRNL REMARK REVDAT 1 12-APR-17 5MGJ 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 10359 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) : 0.192 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.480 REMARK 3 FREE R VALUE TEST SET COUNT : 568 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 31.3408 - 3.3327 1.00 2491 164 0.1622 0.1930 REMARK 3 2 3.3327 - 2.6457 1.00 2445 140 0.1998 0.2351 REMARK 3 3 2.6457 - 2.3114 1.00 2435 129 0.2203 0.2250 REMARK 3 4 2.3114 - 2.1001 1.00 2420 135 0.2505 0.3213 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.97 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 : 0.007 895 REMARK 3 ANGLE : 1.009 1207 REMARK 3 CHIRALITY : 0.035 120 REMARK 3 PLANARITY : 0.006 159 REMARK 3 DIHEDRAL : 13.959 331 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 1796 THROUGH 1810 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.5012 -20.5182 40.3088 REMARK 3 T TENSOR REMARK 3 T11: 0.1940 T22: 0.2213 REMARK 3 T33: 0.2818 T12: -0.1294 REMARK 3 T13: -0.0339 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 0.0119 L22: 0.0062 REMARK 3 L33: 0.0802 L12: -0.0023 REMARK 3 L13: 0.0258 L23: 0.0054 REMARK 3 S TENSOR REMARK 3 S11: -0.0319 S12: -0.0317 S13: 0.0808 REMARK 3 S21: 0.0402 S22: -0.0691 S23: 0.0712 REMARK 3 S31: -0.0806 S32: 0.0152 S33: -0.0211 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1811 THROUGH 1829 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4390 -36.9540 29.5009 REMARK 3 T TENSOR REMARK 3 T11: 0.0950 T22: 0.3960 REMARK 3 T33: 0.1844 T12: -0.1029 REMARK 3 T13: -0.0076 T23: 0.0463 REMARK 3 L TENSOR REMARK 3 L11: 0.0296 L22: 0.0280 REMARK 3 L33: 0.0179 L12: -0.0104 REMARK 3 L13: 0.0057 L23: -0.0090 REMARK 3 S TENSOR REMARK 3 S11: -0.0052 S12: -0.0610 S13: 0.0291 REMARK 3 S21: 0.0224 S22: -0.0463 S23: -0.0488 REMARK 3 S31: -0.0022 S32: 0.0074 S33: -0.0779 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1830 THROUGH 1872 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8949 -28.3172 28.3403 REMARK 3 T TENSOR REMARK 3 T11: 0.1540 T22: 0.3111 REMARK 3 T33: 0.2181 T12: -0.1558 REMARK 3 T13: -0.0393 T23: 0.0911 REMARK 3 L TENSOR REMARK 3 L11: 0.0012 L22: 0.1793 REMARK 3 L33: 0.1300 L12: -0.0046 REMARK 3 L13: -0.0025 L23: -0.1110 REMARK 3 S TENSOR REMARK 3 S11: -0.0866 S12: 0.2117 S13: 0.1289 REMARK 3 S21: -0.0194 S22: -0.0398 S23: 0.0854 REMARK 3 S31: -0.0704 S32: 0.0618 S33: -0.1801 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1873 THROUGH 1898 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0545 -34.9518 40.1774 REMARK 3 T TENSOR REMARK 3 T11: 0.0819 T22: 0.2166 REMARK 3 T33: 0.1419 T12: -0.0906 REMARK 3 T13: 0.0100 T23: -0.0280 REMARK 3 L TENSOR REMARK 3 L11: 0.0104 L22: 0.0239 REMARK 3 L33: 0.2424 L12: -0.0125 REMARK 3 L13: 0.0190 L23: -0.0141 REMARK 3 S TENSOR REMARK 3 S11: 0.0139 S12: -0.0351 S13: 0.0706 REMARK 3 S21: 0.0385 S22: 0.0191 S23: 0.0580 REMARK 3 S31: 0.0390 S32: 0.0232 S33: -0.0027 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 5MGJ 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_1200002438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10377 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.20600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 1.07400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 65.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 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 10.98667 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 21.97333 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 21.97333 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 10.98667 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: 6320 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 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 PHE A1897 -51.77 -127.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7MX A 1901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5MGE RELATED DB: PDB REMARK 900 5MGE CONTAINS THE SAME LIGAND BOUND TO A DIFFERENT BROMODOMAIN REMARK 900 (BAZ2B). DBREF 5MGJ A 1796 1898 UNP Q9UIF9 BAZ2A_HUMAN 1796 1898 SEQADV 5MGJ SER A 1794 UNP Q9UIF9 EXPRESSION TAG SEQADV 5MGJ 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 7MX A1901 14 HETNAM 7MX ETHYL 4-CHLORANYL-1-METHYL-6-OXIDANYLIDENE-PYRIDINE-3- HETNAM 2 7MX CARBOXYLATE FORMUL 2 7MX C9 H10 CL N O3 FORMUL 3 HOH *124(H2 O) HELIX 1 AA1 HIS A 1796 SER A 1811 1 16 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 ARG A 1849 1 11 HELIX 5 AA5 SER A 1854 ASN A 1873 1 20 HELIX 6 AA6 SER A 1877 GLU A 1896 1 20 SITE 1 AC1 8 TRP A1816 PRO A1817 VAL A1822 VAL A1827 SITE 2 AC1 8 TYR A1830 ASN A1873 HOH A2006 HOH A2037 CRYST1 95.737 95.737 32.960 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 0.010445 0.006031 0.000000 0.00000 SCALE2 0.000000 0.012061 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030340 0.00000