HEADER TRANSCRIPTION 04-FEB-17 5N13 TITLE SECOND BROMODOMAIN (BD2) FROM CANDIDA ALBICANS BDF1 IN THE UNBOUND TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 5476; SOURCE 5 GENE: BDF1, CAO19.8593, CAO19.978; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.MIETTON,E.FERRI,M.CHAMPLEBOUXM,N.ZALA,D.MAUBON,Y.ZHOU,M.HARBUT, AUTHOR 2 D.SPITTLER,C.GARNAUD,M.COURCON,M.CHAUVEL,C.D'ENFERT,B.A.KASHEMIROV, AUTHOR 3 M.HULL,M.CORNET,C.E.MCKENNA,J.GOVIN,C.PETOSA REVDAT 3 17-JAN-24 5N13 1 REMARK REVDAT 2 06-SEP-17 5N13 1 REMARK REVDAT 1 31-MAY-17 5N13 0 JRNL AUTH F.MIETTON,E.FERRI,M.CHAMPLEBOUX,N.ZALA,D.MAUBON,Y.ZHOU, JRNL AUTH 2 M.HARBUT,D.SPITTLER,C.GARNAUD,M.COURCON,M.CHAUVEL, JRNL AUTH 3 C.D'ENFERT,B.A.KASHEMIROV,M.HULL,M.CORNET,C.E.MCKENNA, JRNL AUTH 4 J.GOVIN,C.PETOSA JRNL TITL SELECTIVE BET BROMODOMAIN INHIBITION AS AN ANTIFUNGAL JRNL TITL 2 THERAPEUTIC STRATEGY. JRNL REF NAT COMMUN V. 8 15482 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28516956 JRNL DOI 10.1038/NCOMMS15482 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155) 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 39353 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1980 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 38.2725 - 2.8918 1.00 2910 162 0.1700 0.1676 REMARK 3 2 2.8918 - 2.2954 1.00 2781 143 0.1603 0.1717 REMARK 3 3 2.2954 - 2.0053 1.00 2791 134 0.1338 0.1601 REMARK 3 4 2.0053 - 1.8219 1.00 2690 167 0.1327 0.1412 REMARK 3 5 1.8219 - 1.6913 1.00 2715 147 0.1225 0.1366 REMARK 3 6 1.6913 - 1.5916 1.00 2727 159 0.1057 0.1197 REMARK 3 7 1.5916 - 1.5119 1.00 2701 123 0.1042 0.1394 REMARK 3 8 1.5119 - 1.4461 1.00 2727 130 0.1052 0.1441 REMARK 3 9 1.4461 - 1.3904 1.00 2666 155 0.1160 0.1252 REMARK 3 10 1.3904 - 1.3424 1.00 2683 161 0.1188 0.1645 REMARK 3 11 1.3424 - 1.3005 1.00 2683 137 0.1215 0.1503 REMARK 3 12 1.3005 - 1.2633 0.98 2628 126 0.1381 0.1408 REMARK 3 13 1.2633 - 1.2300 0.91 2467 127 0.1450 0.1822 REMARK 3 14 1.2300 - 1.2000 0.82 2204 109 0.1737 0.2286 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.310 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 : 0.004 907 REMARK 3 ANGLE : 0.763 1222 REMARK 3 CHIRALITY : 0.073 128 REMARK 3 PLANARITY : 0.006 160 REMARK 3 DIHEDRAL : 11.710 339 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 5N13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003389. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-13 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 : 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) : 0.9724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39415 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 45.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 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 (%) : 83.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 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: 2OUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL (PH 8.5) AND 1 M REMARK 280 AMMONIUM PHOSPHATE., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.37700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.91400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.59800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.91400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.37700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.59800 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: 550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 ASN A 491 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 669 O HOH A 756 2.10 REMARK 500 OE1 GLU A 454 O HOH A 601 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 791 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 792 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 793 DISTANCE = 6.98 ANGSTROMS REMARK 525 HOH A 794 DISTANCE = 7.95 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 DBREF 5N13 A 386 491 UNP Q5A4W8 BDF1_CANAL 386 491 SEQADV 5N13 ALA A 383 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N13 MET A 384 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N13 GLY A 385 UNP Q5A4W8 EXPRESSION TAG SEQRES 1 A 109 ALA MET GLY ALA ALA GLU LEU ARG PHE CYS ASN GLN THR SEQRES 2 A 109 ILE LYS GLU LEU MET SER LYS LYS HIS TYR ASN TYR ASN SEQRES 3 A 109 PHE PRO PHE LEU ALA PRO VAL ASP THR VAL ALA LEU ASN SEQRES 4 A 109 ILE PRO ASN TYR ASN GLU ILE VAL LYS GLN PRO MET ASP SEQRES 5 A 109 LEU GLY THR ILE GLN SER LYS LEU ALA ASN ASN GLU TYR SEQRES 6 A 109 GLU ASN ALA ASP ASP PHE GLU LYS ASP VAL ARG LEU VAL SEQRES 7 A 109 PHE LYS ASN CYS TYR LEU PHE ASN PRO GLU GLY THR ASP SEQRES 8 A 109 VAL ASN MET MET GLY HIS ARG LEU GLU ALA VAL PHE ASP SEQRES 9 A 109 LYS LYS TRP ALA ASN HET GOL A 501 6 HET GOL A 502 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *194(H2 O) HELIX 1 AA1 GLY A 385 SER A 401 1 17 HELIX 2 AA2 HIS A 404 PHE A 409 1 6 HELIX 3 AA3 PRO A 410 LEU A 412 5 3 HELIX 4 AA4 ASN A 424 VAL A 429 1 6 HELIX 5 AA5 ASP A 434 ASN A 444 1 11 HELIX 6 AA6 ASN A 449 ASN A 468 1 20 HELIX 7 AA7 THR A 472 ALA A 490 1 19 SITE 1 AC1 9 PHE A 411 ASN A 463 CYS A 464 PHE A 467 SITE 2 AC1 9 ASN A 468 HOH A 604 HOH A 607 HOH A 637 SITE 3 AC1 9 HOH A 654 SITE 1 AC2 10 PHE A 409 PRO A 410 LEU A 412 ALA A 413 SITE 2 AC2 10 PRO A 414 ASP A 416 GLU A 446 HOH A 641 SITE 3 AC2 10 HOH A 674 HOH A 717 CRYST1 38.754 45.196 71.828 90.00 90.00 90.00 P 21 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 0.025804 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013922 0.00000