HEADER OXIDOREDUCTASE 30-SEP-13 4MZB TITLE CRYSTAL STRUCTURE OF GRX1 FROM PLASMODIUM FALCIPARUM 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, PFC0271C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1007065; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS GLUTATHIONE, SULFUR-SAD, ACTIVE SITE, PLASTICITY, TRX FOLD, REDOX KEYWDS 2 ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.YOGAVEL,A.SHARMA REVDAT 6 20-NOV-24 4MZB 1 REMARK REVDAT 5 20-SEP-23 4MZB 1 REMARK REVDAT 4 09-SEP-20 4MZB 1 TITLE REMARK REVDAT 3 24-SEP-14 4MZB 1 JRNL REVDAT 2 08-JAN-14 4MZB 1 JRNL REVDAT 1 09-OCT-13 4MZB 0 SPRSDE 09-OCT-13 4MZB 4KJE JRNL AUTH M.YOGAVEL,T.TRIPATHI,A.GUPTA,M.M.BANDAY,S.RAHLFS,K.BECKER, JRNL AUTH 2 H.BELRHALI,A.SHARMA JRNL TITL ATOMIC RESOLUTION CRYSTAL STRUCTURE OF GLUTAREDOXIN 1 FROM JRNL TITL 2 PLASMODIUM FALCIPARUM AND COMPARISON WITH OTHER JRNL TITL 3 GLUTAREDOXINS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 91 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24419382 JRNL DOI 10.1107/S1399004713025285 REMARK 2 REMARK 2 RESOLUTION. 1.04 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) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 53603 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.118 REMARK 3 FREE R VALUE : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2722 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 23.0284 - 2.7693 1.00 2874 148 0.1505 0.1534 REMARK 3 2 2.7693 - 2.1987 1.00 2769 130 0.1316 0.1496 REMARK 3 3 2.1987 - 1.9209 1.00 2707 146 0.1190 0.1277 REMARK 3 4 1.9209 - 1.7453 1.00 2728 141 0.1175 0.1397 REMARK 3 5 1.7453 - 1.6203 1.00 2678 140 0.1107 0.1152 REMARK 3 6 1.6203 - 1.5248 1.00 2684 161 0.0979 0.1042 REMARK 3 7 1.5248 - 1.4484 1.00 2664 135 0.0934 0.1052 REMARK 3 8 1.4484 - 1.3854 1.00 2682 145 0.0944 0.1147 REMARK 3 9 1.3854 - 1.3320 1.00 2639 152 0.0934 0.1049 REMARK 3 10 1.3320 - 1.2861 1.00 2684 131 0.0935 0.1128 REMARK 3 11 1.2861 - 1.2459 1.00 2671 140 0.0916 0.1136 REMARK 3 12 1.2459 - 1.2103 1.00 2656 137 0.0945 0.1021 REMARK 3 13 1.2103 - 1.1784 1.00 2666 143 0.0896 0.1051 REMARK 3 14 1.1784 - 1.1497 1.00 2607 152 0.0889 0.0948 REMARK 3 15 1.1497 - 1.1235 1.00 2633 164 0.0895 0.1080 REMARK 3 16 1.1235 - 1.0996 1.00 2666 141 0.0941 0.1128 REMARK 3 17 1.0996 - 1.0776 1.00 2641 145 0.1025 0.1161 REMARK 3 18 1.0776 - 1.0573 1.00 2631 133 0.1064 0.1354 REMARK 3 19 1.0573 - 1.0380 0.98 2601 138 0.1326 0.1450 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.35 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 1017 REMARK 3 ANGLE : 1.384 1386 REMARK 3 CHIRALITY : 0.071 152 REMARK 3 PLANARITY : 0.006 180 REMARK 3 DIHEDRAL : 19.301 433 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 4MZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.82656 REMARK 200 MONOCHROMATOR : SI(III) CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53655 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.038 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 52.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 21.30 REMARK 200 R MERGE FOR SHELL (I) : 0.51200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 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: PDB ENTRY 4HJM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% W/V PEG1000, 12.5% W/V PEG3350, REMARK 280 12.5% V/V MPD, 0.02 M AMINO ACIDS, 0.1 M MOPS/HEPES SODIUM, PH REMARK 280 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 54.96667 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 27.48333 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 27.48333 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 54.96667 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 465 THR A 4 REMARK 465 SER A 5 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 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 -7.70 73.05 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HJM RELATED DB: PDB REMARK 900 RELATED ID: 3C1R RELATED DB: PDB REMARK 900 RELATED ID: 3CTG RELATED DB: PDB REMARK 900 RELATED ID: 1KTE RELATED DB: PDB REMARK 900 RELATED ID: 4MZC RELATED DB: PDB DBREF 4MZB 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 28 HET MPD A 202 22 HETNAM MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPO C7 H15 N O4 S FORMUL 3 MPD C6 H14 O2 FORMUL 4 HOH *153(H2 O) HELIX 1 1 GLU A 6 ASN A 19 1 14 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 ARG A 77 N PHE A 24 SHEET 4 A 4 ASP A 83 GLY A 86 -1 O ASP A 83 N ILE A 80 SSBOND 1 CYS A 29 CYS A 32 1555 1555 2.10 CISPEP 1 VAL A 75 PRO A 76 0 5.66 SITE 1 AC1 11 LYS A 9 TYR A 31 TYR A 65 GLU A 68 SITE 2 AC1 11 PRO A 76 GLY A 87 CYS A 88 ASP A 89 SITE 3 AC1 11 HOH A 309 HOH A 317 HOH A 373 SITE 1 AC2 3 ASN A 13 PHE A 79 LYS A 82 CRYST1 47.953 47.953 82.450 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 0.020854 0.012040 0.000000 0.00000 SCALE2 0.000000 0.024080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012129 0.00000