HEADER TRANSCRIPTION 21-NOV-24 9HHC
TITLE CRYSTAL STRUCTURE OF THE PLASMODIUM FALCIPARUM BROMODOMAIN PFBDP1 IN
TITLE 2 COMPLEX WITH MPM2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BROMODOMAIN PROTEIN 1;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM 3D7;
SOURCE 3 ORGANISM_TAXID: 36329;
SOURCE 4 GENE: PF3D7_1033700;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PLASMODIUM, BROMODOMAIN, INHIBITOR, COMPLEX, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR M.AMANN,M.HUEGLE,O.EINSLE,S.GUENTHER
REVDAT 1 02-APR-25 9HHC 0
JRNL AUTH M.AMANN,R.WARSTAT,K.K.RECHTEN,P.THEUER,M.SCHUSTEREDER,
JRNL AUTH 2 S.CLAVEY,B.BREIT,O.EINSLE,M.HUGLE,M.PETTER,S.GUNTHER
JRNL TITL A NOVEL INHIBITOR AGAINST THE BROMODOMAIN PROTEIN 1 OF THE
JRNL TITL 2 MALARIA PATHOGEN PLASMODIUM FALCIPARUM.
JRNL REF CHEMMEDCHEM 00024 2025
JRNL REFN ESSN 1860-7187
JRNL PMID 40099623
JRNL DOI 10.1002/CMDC.202500024
REMARK 2
REMARK 2 RESOLUTION. 1.56 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.21_5207
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.56
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.36
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 53.0
REMARK 3 NUMBER OF REFLECTIONS : 13882
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.200
REMARK 3 R VALUE (WORKING SET) : 0.198
REMARK 3 FREE R VALUE : 0.237
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050
REMARK 3 FREE R VALUE TEST SET COUNT : 701
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 43.3600 - 2.6600 0.95 4903 270 0.1804 0.2270
REMARK 3 2 2.6600 - 2.1100 0.72 3571 190 0.2248 0.2664
REMARK 3 3 2.1100 - 1.8500 0.50 2463 133 0.2390 0.2473
REMARK 3 4 1.8500 - 1.6800 0.33 1626 73 0.2899 0.2474
REMARK 3 5 1.6800 - 1.5600 0.13 618 35 0.2681 0.2316
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
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) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.610
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 : 0.006 1113
REMARK 3 ANGLE : 0.759 1515
REMARK 3 CHIRALITY : 0.045 164
REMARK 3 PLANARITY : 0.004 192
REMARK 3 DIHEDRAL : 17.072 403
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 3.1697 19.7688 13.0079
REMARK 3 T TENSOR
REMARK 3 T11: 0.1460 T22: 0.1749
REMARK 3 T33: 0.1441 T12: 0.0396
REMARK 3 T13: -0.0020 T23: 0.0653
REMARK 3 L TENSOR
REMARK 3 L11: 3.0407 L22: 0.8028
REMARK 3 L33: 3.2944 L12: -0.3484
REMARK 3 L13: -0.5438 L23: 0.3729
REMARK 3 S TENSOR
REMARK 3 S11: -0.1623 S12: 0.0612 S13: -0.2642
REMARK 3 S21: -0.0740 S22: 0.0292 S23: -0.1143
REMARK 3 S31: 0.1513 S32: 0.2214 S33: 0.1116
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 9HHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-24.
REMARK 100 THE DEPOSITION ID IS D_1292143302.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 18-OCT-21
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 : SLS
REMARK 200 BEAMLINE : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC
REMARK 200 DATA SCALING SOFTWARE : STARANISO
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13888
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.558
REMARK 200 RESOLUTION RANGE LOW (A) : 67.575
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 89.5
REMARK 200 DATA REDUNDANCY : 13.00
REMARK 200 R MERGE (I) : 0.22100
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
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 <I/SIGMA(I)> FOR SHELL : 1.400
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: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.58
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2M LISO4, 0.1 M TRIS PH
REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2
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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 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 19.18000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.36000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.91000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.18000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.36000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.91000
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.18000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.36000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.91000
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.18000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.36000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.91000
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 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 GLY A 324
REMARK 465 PRO A 325
REMARK 465 LEU A 326
REMARK 465 GLY A 327
REMARK 465 GLU A 457
REMARK 465 GLU A 458
REMARK 465 GLU A 459
REMARK 465 ASN A 460
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 GLU A 330 CG CD OE1 OE2
REMARK 470 LYS A 363 CG CD CE NZ
REMARK 470 LYS A 364 CG CD CE NZ
REMARK 470 ASN A 366 CG OD1 ND2
REMARK 470 LYS A 388 CE NZ
REMARK 470 LYS A 400 NZ
REMARK 470 LYS A 445 CD CE NZ
REMARK 470 LYS A 447 CG CD CE NZ
REMARK 470 MET A 452 SD CE
REMARK 470 LYS A 454 CG CD CE NZ
REMARK 470 LEU A 455 CG CD1 CD2
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 678 O HOH A 709 2.11
REMARK 500 O HOH A 663 O HOH A 672 2.12
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 9HGF RELATED DB: PDB
DBREF 9HHC A 333 460 UNP Q8IJ72 Q8IJ72_PLAF7 333 460
SEQADV 9HHC GLY A 324 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC PRO A 325 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC LEU A 326 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC GLY A 327 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC SER A 328 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC PRO A 329 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC GLU A 330 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC PHE A 331 UNP Q8IJ72 EXPRESSION TAG
SEQADV 9HHC MET A 332 UNP Q8IJ72 EXPRESSION TAG
SEQRES 1 A 137 GLY PRO LEU GLY SER PRO GLU PHE MET ASN LYS GLN TRP
SEQRES 2 A 137 TYR LEU LEU ALA ASN GLN LEU ILE LEU SER LEU SER LYS
SEQRES 3 A 137 TYR GLU GLY GLY HIS ILE PHE GLU LYS LEU VAL ASP ALA
SEQRES 4 A 137 LYS LYS GLN ASN CYS PRO ASP TYR TYR ASP VAL ILE LYS
SEQRES 5 A 137 ASN PRO MET SER PHE SER CYS ILE LYS THR LYS LEU LYS
SEQRES 6 A 137 LYS GLY GLN TYR ALA TYR PRO SER GLU PHE VAL LYS ASP
SEQRES 7 A 137 VAL GLN LEU ILE PHE ASP ASN CYS SER LEU TYR ASN THR
SEQRES 8 A 137 SER ASN SER VAL VAL ALA ILE THR GLY LYS ASN ILE GLU
SEQRES 9 A 137 THR TYR PHE ASN ASN GLN LEU ILE VAL MET GLY TYR ASN
SEQRES 10 A 137 ASN PHE ILE LEU LYS GLU LYS LYS ILE ASN ASP MET LEU
SEQRES 11 A 137 LYS LEU VAL GLU GLU GLU ASN
HET BU3 A 501 6
HET I5K A 502 38
HETNAM BU3 (R,R)-2,3-BUTANEDIOL
HETNAM I5K 1-(3-AMINOPHENYL)-3-METHYL-5,6,7,8-TETRAHYDRO-2~{H}-
HETNAM 2 I5K CYCLOHEPTA[C]PYRROL-4-ONE
FORMUL 2 BU3 C4 H10 O2
FORMUL 3 I5K C16 H18 N2 O
FORMUL 4 HOH *124(H2 O)
HELIX 1 AA1 SER A 328 TYR A 350 1 23
HELIX 2 AA2 GLY A 352 GLU A 357 5 6
HELIX 3 AA3 ASP A 369 ILE A 374 1 6
HELIX 4 AA4 SER A 379 LYS A 389 1 11
HELIX 5 AA5 TYR A 394 ASN A 413 1 20
HELIX 6 AA6 SER A 417 MET A 437 1 21
HELIX 7 AA7 GLY A 438 VAL A 456 1 19
CRYST1 38.360 86.720 107.820 90.00 90.00 90.00 I 2 2 2 8
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 0.026069 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011531 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009275 0.00000