HEADER TRANSCRIPTION 22-NOV-23 8R6I TITLE CRYSTAL STRUCTURE OF CANDIDA GLABRATA BDF1 BROMODOMAIN 1 IN THE TITLE 2 UNBOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CANDIDA GLABRATA STRAIN CBS138 CHROMOSOME C COMPLETE COMPND 3 SEQUENCE; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAKASEOMYCES GLABRATUS; SOURCE 3 ORGANISM_TAXID: 5478; SOURCE 4 GENE: CAGL0C02541G; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BROMODOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.PETOSA,K.WEI,C.E.MCKENNA,J.GOVIN REVDAT 2 29-JAN-25 8R6I 1 JRNL REVDAT 1 30-OCT-24 8R6I 0 JRNL AUTH K.WEI,M.ARLOTTO,J.M.OVERHULSE,T.A.DINH,Y.ZHOU,N.J.DUPPER, JRNL AUTH 2 J.YANG,B.A.KASHEMIROV,H.DAWI,C.GARNAUD,G.BOURGINE,F.MIETTON, JRNL AUTH 3 M.CHAMPLEBOUX,A.LARABI,Y.HAYAT,R.L.INDORATO, JRNL AUTH 4 M.NOIRCLERC-SAVOYE,D.SKOUFIAS,M.CORNET,G.RABUT,C.E.MCKENNA, JRNL AUTH 5 C.PETOSA,J.GOVIN JRNL TITL HUMANIZED CANDIDA AND NANOBIT ASSAYS EXPEDITE DISCOVERY OF JRNL TITL 2 BDF1 BROMODOMAIN INHIBITORS WITH ANTIFUNGAL POTENTIAL. JRNL REF ADV SCI 04260 2025 JRNL REFN ESSN 2198-3844 JRNL PMID 39821709 JRNL DOI 10.1002/ADVS.202404260 REMARK 2 REMARK 2 RESOLUTION. 1.08 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 66240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2099 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 48.1900 - 2.6600 0.93 4469 147 0.1450 0.1468 REMARK 3 2 2.6600 - 2.1100 0.91 4363 143 0.1543 0.1896 REMARK 3 3 2.1100 - 1.8400 0.91 4401 144 0.1575 0.1631 REMARK 3 4 1.8400 - 1.6700 0.92 4457 146 0.1637 0.2102 REMARK 3 5 1.6700 - 1.5500 0.91 4387 143 0.1576 0.1925 REMARK 3 6 1.5500 - 1.4600 0.90 4341 142 0.1723 0.2040 REMARK 3 7 1.4600 - 1.3900 0.90 4351 142 0.1857 0.2018 REMARK 3 8 1.3900 - 1.3300 0.90 4330 142 0.1919 0.2505 REMARK 3 9 1.3300 - 1.2800 0.90 4332 141 0.2060 0.2180 REMARK 3 10 1.2800 - 1.2300 0.90 4355 143 0.2169 0.2722 REMARK 3 11 1.2300 - 1.1900 0.88 4199 138 0.2310 0.2530 REMARK 3 12 1.1900 - 1.1600 0.86 4195 137 0.2562 0.2537 REMARK 3 13 1.1600 - 1.1300 0.87 4195 137 0.2683 0.3014 REMARK 3 14 1.1300 - 1.1000 0.87 4211 138 0.2830 0.3318 REMARK 3 15 1.1000 - 1.0800 0.73 3555 116 0.3117 0.2976 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.121 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.69 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 : 0.009 1848 REMARK 3 ANGLE : 1.051 2497 REMARK 3 CHIRALITY : 0.082 274 REMARK 3 PLANARITY : 0.010 333 REMARK 3 DIHEDRAL : 14.742 723 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 8R6I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292134503. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-18 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 : 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 : 66240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 48.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 1500 AND 0.1 MIB REMARK 280 (MALONIC ACID:IMIDAZOLE:BORIC ACID IN 2:3:3 MOLAR RATIO) BUFFER REMARK 280 (PH 9)., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 GLY B 124 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 B 445 O HOH B 486 1.98 REMARK 500 O HOH A 446 O HOH A 477 2.02 REMARK 500 O HOH B 354 O HOH B 368 2.05 REMARK 500 O HOH A 376 O HOH A 458 2.12 REMARK 500 O HOH B 322 O HOH B 454 2.13 REMARK 500 O HOH A 393 O HOH A 482 2.13 REMARK 500 O HOH B 487 O HOH B 489 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 434 O HOH B 452 1556 2.10 REMARK 500 O HOH A 483 O HOH B 499 1545 2.11 REMARK 500 O HOH B 344 O HOH B 392 1655 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 8R6I A 128 237 UNP Q6FWV7 Q6FWV7_CANGA 108 217 DBREF 8R6I B 128 237 UNP Q6FWV7 Q6FWV7_CANGA 108 217 SEQADV 8R6I GLY A 124 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I ALA A 125 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I MET A 126 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I GLY A 127 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I GLY B 124 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I ALA B 125 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I MET B 126 UNP Q6FWV7 EXPRESSION TAG SEQADV 8R6I GLY B 127 UNP Q6FWV7 EXPRESSION TAG SEQRES 1 A 114 GLY ALA MET GLY ILE PRO GLN HIS GLN GLN LYS HIS ALA SEQRES 2 A 114 LEU MET ALA ILE LYS ALA VAL LYS ARG LEU LYS ASP ALA SEQRES 3 A 114 ARG PRO PHE LEU GLN PRO VAL ASP PRO VAL ALA LEU ASN SEQRES 4 A 114 ILE PRO LEU TYR PHE ASN PHE ILE LYS ARG PRO MET ASP SEQRES 5 A 114 LEU GLN THR ILE GLU ARG LYS LEU ASN ALA ASN ALA TYR SEQRES 6 A 114 GLU THR PRO GLU GLN ILE THR GLU ASP PHE ASN LEU MET SEQRES 7 A 114 VAL GLU ASN SER ALA LYS PHE ASN GLY PRO THR ALA VAL SEQRES 8 A 114 ILE THR GLN MET GLY ARG ASN ILE GLN ALA ALA PHE GLU SEQRES 9 A 114 LYS HIS MET LEU ASN MET PRO ALA LYS ASP SEQRES 1 B 114 GLY ALA MET GLY ILE PRO GLN HIS GLN GLN LYS HIS ALA SEQRES 2 B 114 LEU MET ALA ILE LYS ALA VAL LYS ARG LEU LYS ASP ALA SEQRES 3 B 114 ARG PRO PHE LEU GLN PRO VAL ASP PRO VAL ALA LEU ASN SEQRES 4 B 114 ILE PRO LEU TYR PHE ASN PHE ILE LYS ARG PRO MET ASP SEQRES 5 B 114 LEU GLN THR ILE GLU ARG LYS LEU ASN ALA ASN ALA TYR SEQRES 6 B 114 GLU THR PRO GLU GLN ILE THR GLU ASP PHE ASN LEU MET SEQRES 7 B 114 VAL GLU ASN SER ALA LYS PHE ASN GLY PRO THR ALA VAL SEQRES 8 B 114 ILE THR GLN MET GLY ARG ASN ILE GLN ALA ALA PHE GLU SEQRES 9 B 114 LYS HIS MET LEU ASN MET PRO ALA LYS ASP FORMUL 3 HOH *390(H2 O) HELIX 1 AA1 PRO A 129 ARG A 145 1 17 HELIX 2 AA2 LEU A 146 LEU A 153 5 8 HELIX 3 AA3 LEU A 165 ILE A 170 1 6 HELIX 4 AA4 ASP A 175 ALA A 185 1 11 HELIX 5 AA5 THR A 190 ASN A 209 1 20 HELIX 6 AA6 ALA A 213 ASN A 232 1 20 HELIX 7 AA7 PRO B 129 ARG B 145 1 17 HELIX 8 AA8 LEU B 146 LEU B 153 5 8 HELIX 9 AA9 LEU B 165 ILE B 170 1 6 HELIX 10 AB1 ASP B 175 ALA B 185 1 11 HELIX 11 AB2 THR B 190 ASN B 209 1 20 HELIX 12 AB3 ALA B 213 LEU B 231 1 19 CRYST1 22.890 40.593 48.872 98.14 94.37 94.77 P 1 2 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 0.043687 0.003645 0.003925 0.00000 SCALE2 0.000000 0.024720 0.003722 0.00000 SCALE3 0.000000 0.000000 0.020753 0.00000