HEADER NUCLEAR PROTEIN 30-MAR-21 7M97 TITLE CRYSTAL STRUCTURE OF THE BROMODOMAIN FROM PLASMODIUM FALCIPARUM TITLE 2 BROMODOMAIN PROTEIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: ISOLATE 3D7; SOURCE 5 GENE: PF3D7_1033700; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BROMODOMAIN, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.C.GLASS REVDAT 2 18-OCT-23 7M97 1 REMARK REVDAT 1 26-MAY-21 7M97 0 JRNL AUTH S.ALKRIMI,M.PHILLIPS,J.C.NIX,K.C.GLASS JRNL TITL CRYSTAL STRUCTURE OF THE BROMODOMAIN FROM PLASMODIUM JRNL TITL 2 FALCIPARUM BROMODOMAIN PROTEIN 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12572 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 587 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 35.8400 - 3.1700 1.00 3125 146 0.1744 0.2005 REMARK 3 2 3.1700 - 2.5200 1.00 2983 160 0.2091 0.2593 REMARK 3 3 2.5200 - 2.2000 1.00 2957 148 0.2104 0.2651 REMARK 3 4 2.2000 - 2.0000 0.99 2920 133 0.2430 0.3180 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) : 0.187 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.831 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.01 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 : 0.008 1028 REMARK 3 ANGLE : 0.889 1394 REMARK 3 CHIRALITY : 0.054 157 REMARK 3 PLANARITY : 0.004 176 REMARK 3 DIHEDRAL : 20.795 376 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): 34.9864 20.3869 40.5860 REMARK 3 T TENSOR REMARK 3 T11: 0.2425 T22: 0.3338 REMARK 3 T33: 0.1909 T12: -0.0656 REMARK 3 T13: -0.0112 T23: -0.0539 REMARK 3 L TENSOR REMARK 3 L11: 4.3622 L22: 1.6923 REMARK 3 L33: 5.0968 L12: 0.0933 REMARK 3 L13: -1.2648 L23: -0.3672 REMARK 3 S TENSOR REMARK 3 S11: -0.1893 S12: -0.0265 S13: -0.1906 REMARK 3 S21: 0.0786 S22: 0.0515 S23: 0.1185 REMARK 3 S31: 0.1688 S32: -0.1939 S33: 0.1350 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 7M97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255691. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02602 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26720 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.930 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: 5ULC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M LITHIUM SULFATE, 0.1 M TRIS, PH REMARK 280 8.5, 38% PEG400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 19.02550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.33350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.39850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.02550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.33350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.39850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.02550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.33350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.39850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.02550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.33350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.39850 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 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 328 REMARK 465 PRO A 329 REMARK 465 LEU A 330 REMARK 465 GLY A 331 REMARK 465 SER A 332 REMARK 465 GLU A 457 REMARK 465 SER A 458 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 LYS A 363 CG CD CE NZ REMARK 470 LYS A 364 CG CD CE NZ REMARK 470 GLN A 365 CG CD OE1 NE2 REMARK 470 ASN A 366 CG OD1 ND2 REMARK 470 LYS A 447 CG CD CE NZ REMARK 470 LYS A 454 CG CD CE NZ 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 LEU A 455 41.41 -90.46 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 609 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 610 DISTANCE = 6.88 ANGSTROMS DBREF 7M97 A 333 458 UNP Q8IJ72 Q8IJ72_PLAF7 333 458 SEQADV 7M97 GLY A 328 UNP Q8IJ72 EXPRESSION TAG SEQADV 7M97 PRO A 329 UNP Q8IJ72 EXPRESSION TAG SEQADV 7M97 LEU A 330 UNP Q8IJ72 EXPRESSION TAG SEQADV 7M97 GLY A 331 UNP Q8IJ72 EXPRESSION TAG SEQADV 7M97 SER A 332 UNP Q8IJ72 EXPRESSION TAG SEQADV 7M97 SER A 458 UNP Q8IJ72 GLU 458 ENGINEERED MUTATION SEQRES 1 A 131 GLY PRO LEU GLY SER ASN LYS GLN TRP TYR LEU LEU ALA SEQRES 2 A 131 ASN GLN LEU ILE LEU SER LEU SER LYS TYR GLU GLY GLY SEQRES 3 A 131 HIS ILE PHE GLU LYS LEU VAL ASP ALA LYS LYS GLN ASN SEQRES 4 A 131 CYS PRO ASP TYR TYR ASP VAL ILE LYS ASN PRO MET SER SEQRES 5 A 131 PHE SER CYS ILE LYS THR LYS LEU LYS LYS GLY GLN TYR SEQRES 6 A 131 ALA TYR PRO SER GLU PHE VAL LYS ASP VAL GLN LEU ILE SEQRES 7 A 131 PHE ASP ASN CYS SER LEU TYR ASN THR SER ASN SER VAL SEQRES 8 A 131 VAL ALA ILE THR GLY LYS ASN ILE GLU THR TYR PHE ASN SEQRES 9 A 131 ASN GLN LEU ILE VAL MET GLY TYR ASN ASN PHE ILE LEU SEQRES 10 A 131 LYS GLU LYS LYS ILE ASN ASP MET LEU LYS LEU VAL GLU SEQRES 11 A 131 SER FORMUL 2 HOH *110(H2 O) HELIX 1 AA1 ASN A 333 TYR A 350 1 18 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 LEU A 455 1 18 CRYST1 38.051 88.667 106.797 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 0.026281 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009364 0.00000