HEADER OXIDOREDUCTASE 03-OCT-13 4N11 TITLE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM REDUCED GLUTAREDOXIN 1 TITLE 2 (PFGRX1) COMPLEXED WITH CISPLATIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTAREDOXIN 1; COMPND 5 EC: 1.20.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: GRX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS GLUTATHIONE, ACTIVE SITE, TRX FOLD, REDOX ENZYME, PT-SAD, CISPLATIN, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.YOGAVEL,A.SHARMA REVDAT 3 20-MAR-24 4N11 1 REMARK REVDAT 2 15-NOV-17 4N11 1 REMARK REVDAT 1 08-OCT-14 4N11 0 JRNL AUTH M.YOGAVEL,T.TRIPATHI,S.RAHLFS,K.BECKER,A.SHARMA JRNL TITL INTERACTION OF CISPLATIN WITH PLASMODIUM FALCIPARUM JRNL TITL 2 GLUTAREDOXIN 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT : 821 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 27.4663 - 3.5780 1.00 1350 133 0.1647 0.2181 REMARK 3 2 3.5780 - 2.8409 1.00 1254 139 0.1573 0.1997 REMARK 3 3 2.8409 - 2.4821 1.00 1249 142 0.1497 0.2219 REMARK 3 4 2.4821 - 2.2553 1.00 1242 131 0.1429 0.1833 REMARK 3 5 2.2553 - 2.0937 1.00 1217 127 0.1456 0.1994 REMARK 3 6 2.0937 - 1.9703 1.00 1213 149 0.1611 0.2126 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.46 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 : 0.010 945 REMARK 3 ANGLE : 1.327 1276 REMARK 3 CHIRALITY : 0.082 141 REMARK 3 PLANARITY : 0.004 159 REMARK 3 DIHEDRAL : 16.479 374 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 4N11 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5%(W/V) PEG1000, 12.5%(W/V) REMARK 280 PEG3350, 12.5%(V/V) MPD, 0.02M AMINO ACIDS, 0.1M MOPS/HEPES REMARK 280 SODIUM,, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.92733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.46367 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.46367 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.92733 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 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 THR A 4 OG1 CG2 REMARK 470 GLU A 6 CG CD OE1 OE2 REMARK 470 ASN A 111 CG OD1 ND2 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 LYS A 82 -11.46 76.66 REMARK 500 LYS A 82 -11.07 76.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 204 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 26 NZ REMARK 620 2 CPT A 204 N1 90.5 REMARK 620 3 CPT A 204 N2 107.1 86.5 REMARK 620 4 CPT A 204 CL1 75.3 92.1 177.2 REMARK 620 5 CYS A 29 SG 91.6 167.7 81.3 100.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 204 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 29 SG REMARK 620 2 CPT A 204 N1 167.5 REMARK 620 3 CPT A 204 N2 81.2 86.4 REMARK 620 4 CPT A 204 CL1 100.3 92.1 176.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT A 204 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 29 SG REMARK 620 2 CPT A 204 N1 167.5 REMARK 620 3 CPT A 204 N2 81.2 86.4 REMARK 620 4 CPT A 204 CL1 100.3 92.1 176.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HJM RELATED DB: PDB REMARK 900 RELATED ID: 4MZB RELATED DB: PDB REMARK 900 RELATED ID: 4MZC RELATED DB: PDB REMARK 900 RELATED ID: 1KTE RELATED DB: PDB REMARK 900 RELATED ID: 3C1R RELATED DB: PDB REMARK 900 RELATED ID: 3CTG RELATED DB: PDB REMARK 900 RELATED ID: 4N0Z RELATED DB: PDB REMARK 900 RELATED ID: 4N10 RELATED DB: PDB DBREF 4N11 A 1 111 UNP Q9NLB2 Q9NLB2_PLAF7 1 111 SEQRES 1 A 111 MET ALA GLY THR SER GLU ALA VAL LYS LYS TRP VAL ASN SEQRES 2 A 111 LYS ILE ILE GLU GLU ASN ILE ILE ALA VAL PHE ALA LYS SEQRES 3 A 111 THR GLU CYS PRO TYR CYS ILE LYS ALA ILE SER ILE LEU SEQRES 4 A 111 LYS GLY TYR ASN LEU ASN SER HIS MET HIS VAL GLU ASN SEQRES 5 A 111 ILE GLU LYS ASN PRO ASP MET ALA ASN ILE GLN ALA TYR SEQRES 6 A 111 LEU LYS GLU LEU THR GLY LYS SER SER VAL PRO ARG ILE SEQRES 7 A 111 PHE ILE ASN LYS ASP VAL VAL GLY GLY CYS ASP ASP LEU SEQRES 8 A 111 VAL LYS GLU ASN ASP GLU GLY LYS LEU LYS GLU ARG LEU SEQRES 9 A 111 GLN LYS LEU GLY LEU VAL ASN HET MPO A 201 13 HET MPD A 202 8 HET MPD A 203 16 HET CPT A 204 11 HETNAM MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 2 MPO C7 H15 N O4 S FORMUL 3 MPD 2(C6 H14 O2) FORMUL 5 CPT CL2 H6 N2 PT FORMUL 6 HOH *80(H2 O) HELIX 1 1 THR A 4 ASN A 19 1 16 HELIX 2 2 CYS A 29 TYR A 42 1 14 HELIX 3 3 ASN A 43 SER A 46 5 4 HELIX 4 4 ASP A 58 GLY A 71 1 14 HELIX 5 5 GLY A 87 GLU A 97 1 11 HELIX 6 6 GLY A 98 LEU A 107 1 10 SHEET 1 A 4 MET A 48 ASN A 52 0 SHEET 2 A 4 ILE A 21 ALA A 25 1 N ALA A 25 O GLU A 51 SHEET 3 A 4 ARG A 77 ILE A 80 -1 O PHE A 79 N ALA A 22 SHEET 4 A 4 ASP A 83 GLY A 86 -1 O ASP A 83 N ILE A 80 LINK NZ ALYS A 26 PT1 ACPT A 204 1555 1555 2.42 LINK SG CYS A 29 PT1 BCPT A 204 1555 1555 2.60 LINK SG CYS A 29 PT1 CCPT A 204 1555 1555 2.60 LINK SG CYS A 29 PT1 ACPT A 204 1555 1555 2.60 CISPEP 1 VAL A 75 PRO A 76 0 0.06 SITE 1 AC1 12 SER A 5 LYS A 9 TYR A 31 TYR A 65 SITE 2 AC1 12 GLU A 68 PRO A 76 GLY A 87 CYS A 88 SITE 3 AC1 12 ASP A 89 HOH A 302 HOH A 327 HOH A 362 SITE 1 AC2 4 ASN A 13 GLU A 17 LYS A 82 HOH A 375 SITE 1 AC3 6 LYS A 26 THR A 27 GLU A 28 ILE A 33 SITE 2 AC3 6 ILE A 36 HOH A 345 SITE 1 AC4 5 LYS A 26 GLU A 28 CYS A 29 VAL A 75 SITE 2 AC4 5 HOH A 377 CRYST1 48.478 48.478 82.391 90.00 90.00 120.00 P 32 2 1 6 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 0.020628 0.011910 0.000000 0.00000 SCALE2 0.000000 0.023819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012137 0.00000