HEADER TRANSCRIPTION 05-FEB-17 5N18 TITLE SECOND BROMODOMAIN (BD2) FROM CANDIDA ALBICANS BDF1 BOUND TO AN TITLE 2 IMIDAZOPYRIDINE (COMPOUND 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN-CONTAINING FACTOR 1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDA ALBICANS (STRAIN SC5314 / ATCC MYA- SOURCE 3 2876); SOURCE 4 ORGANISM_COMMON: YEAST; SOURCE 5 ORGANISM_TAXID: 237561; SOURCE 6 STRAIN: SC5314 / ATCC MYA-2876; SOURCE 7 GENE: BDF1, CAO19.8593, CAO19.978; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.MIETTON,E.FERRI,M.CHAMPLEBOUX,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 4 17-JAN-24 5N18 1 REMARK REVDAT 3 06-SEP-17 5N18 1 ATOM REVDAT 2 07-JUN-17 5N18 1 REMARK REVDAT 1 31-MAY-17 5N18 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 34641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1790 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 44.3070 - 3.4090 0.91 2522 123 0.1571 0.1538 REMARK 3 2 3.4090 - 2.7059 0.92 2460 154 0.1607 0.1931 REMARK 3 3 2.7059 - 2.3639 0.93 2468 144 0.1634 0.2147 REMARK 3 4 2.3639 - 2.1478 0.94 2521 134 0.1495 0.2000 REMARK 3 5 2.1478 - 1.9938 0.95 2511 136 0.1468 0.2015 REMARK 3 6 1.9938 - 1.8763 0.97 2556 139 0.1514 0.1952 REMARK 3 7 1.8763 - 1.7823 0.98 2572 143 0.1485 0.2138 REMARK 3 8 1.7823 - 1.7047 0.94 2512 120 0.1465 0.1950 REMARK 3 9 1.7047 - 1.6391 0.95 2486 133 0.1515 0.2004 REMARK 3 10 1.6391 - 1.5825 0.97 2562 149 0.1634 0.2483 REMARK 3 11 1.5825 - 1.5330 0.97 2584 126 0.1787 0.2244 REMARK 3 12 1.5330 - 1.4892 0.97 2539 146 0.2080 0.2653 REMARK 3 13 1.4892 - 1.4500 0.97 2558 143 0.2306 0.3028 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.290 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 : 0.002 1809 REMARK 3 ANGLE : 0.739 2445 REMARK 3 CHIRALITY : 0.068 252 REMARK 3 PLANARITY : 0.004 321 REMARK 3 DIHEDRAL : 13.249 673 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 5N18 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003395. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9660 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34661 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 44.307 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 2.450 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 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: 5N13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED BY MIXING A REMARK 280 SOLUTION OF 22 MG/ML PROTEIN AND 1.5 MM INHIBITOR WITH 0.1 M REMARK 280 SODIUM ACETATE (PH 4.6) AND 25% (W/V) PEG 3000., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.99850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ALA A 383 REMARK 465 ALA A 490 REMARK 465 ASN A 491 REMARK 465 ALA B 383 REMARK 465 ALA B 490 REMARK 465 ASN B 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 TRP B 489 O HOH B 601 2.15 REMARK 500 O HOH A 700 O HOH A 704 2.17 REMARK 500 O3 GOL B 501 O HOH B 602 2.19 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 8HZ A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 501 DBREF 5N18 A 386 491 UNP Q5A4W8 BDF1_CANAL 386 491 DBREF 5N18 B 386 491 UNP Q5A4W8 BDF1_CANAL 386 491 SEQADV 5N18 ALA A 383 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N18 MET A 384 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N18 GLY A 385 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N18 ALA B 383 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N18 MET B 384 UNP Q5A4W8 EXPRESSION TAG SEQADV 5N18 GLY B 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 SEQRES 1 B 109 ALA MET GLY ALA ALA GLU LEU ARG PHE CYS ASN GLN THR SEQRES 2 B 109 ILE LYS GLU LEU MET SER LYS LYS HIS TYR ASN TYR ASN SEQRES 3 B 109 PHE PRO PHE LEU ALA PRO VAL ASP THR VAL ALA LEU ASN SEQRES 4 B 109 ILE PRO ASN TYR ASN GLU ILE VAL LYS GLN PRO MET ASP SEQRES 5 B 109 LEU GLY THR ILE GLN SER LYS LEU ALA ASN ASN GLU TYR SEQRES 6 B 109 GLU ASN ALA ASP ASP PHE GLU LYS ASP VAL ARG LEU VAL SEQRES 7 B 109 PHE LYS ASN CYS TYR LEU PHE ASN PRO GLU GLY THR ASP SEQRES 8 B 109 VAL ASN MET MET GLY HIS ARG LEU GLU ALA VAL PHE ASP SEQRES 9 B 109 LYS LYS TRP ALA ASN HET 8HZ A 501 25 HET GOL B 501 6 HETNAM 8HZ 4-[8-METHYL-3-[(4-METHYLPHENYL)AMINO]IMIDAZO[1,2- HETNAM 2 8HZ A]PYRIDIN-2-YL]PHENOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 8HZ C21 H19 N3 O FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *273(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 TRP A 489 1 18 HELIX 8 AA8 GLY B 385 SER B 401 1 17 HELIX 9 AA9 HIS B 404 PHE B 409 1 6 HELIX 10 AB1 PRO B 410 LEU B 412 5 3 HELIX 11 AB2 ASN B 424 VAL B 429 1 6 HELIX 12 AB3 ASP B 434 ASN B 444 1 11 HELIX 13 AB4 ASN B 449 ASN B 468 1 20 HELIX 14 AB5 THR B 472 TRP B 489 1 18 SITE 1 AC1 7 LEU A 420 ILE A 422 TYR A 425 PHE A 467 SITE 2 AC1 7 ASN A 468 HOH A 633 HOH A 640 SITE 1 AC2 9 PRO B 410 VAL B 415 TYR B 425 ASN B 468 SITE 2 AC2 9 VAL B 474 HOH B 602 HOH B 625 HOH B 634 SITE 3 AC2 9 HOH B 657 CRYST1 46.484 35.997 64.495 90.00 107.61 90.00 P 1 21 1 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 0.021513 0.000000 0.006826 0.00000 SCALE2 0.000000 0.027780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016267 0.00000