HEADER OXIDOREDUCTASE 06-JUL-16 5KQA TITLE CRYSTAL STRUCTURE OF BUCKWHEAT GLUTAREDOXIN-GLUTATHIONE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-GLUTATHIONE COMPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POLYGONACEAE; SOURCE 3 ORGANISM_COMMON: BUCKWHEAT FAMILY; SOURCE 4 ORGANISM_TAXID: 3615; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS GLUTAREDOXIN, GLUTATHIONE, COMPLEX, MONOMER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,W.WANG,Y.ZHAO,Z.WANG,H.WANG REVDAT 3 08-NOV-23 5KQA 1 REMARK REVDAT 2 27-SEP-17 5KQA 1 REMARK REVDAT 1 05-JUL-17 5KQA 0 JRNL AUTH X.ZHANG,W.WANG,C.LI,Y.ZHAO,H.YUAN,X.TAN,L.WU,Z.WANG,H.WANG JRNL TITL STRUCTURAL INSIGHTS INTO THE BINDING OF BUCKWHEAT JRNL TITL 2 GLUTAREDOXIN WITH GSH AND REGULATION OF ITS CATALYTIC JRNL TITL 3 ACTIVITY JRNL REF J. INORG. BIOCHEM. V. 173 21 2017 JRNL REFN ISSN 1873-3344 JRNL PMID 28478310 JRNL DOI 10.1016/J.JINORGBIO.2017.04.019 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 7380 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 738 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 38.9929 - 3.5052 0.97 1386 154 0.1588 0.1910 REMARK 3 2 3.5052 - 2.7824 0.99 1342 149 0.1726 0.2131 REMARK 3 3 2.7824 - 2.4308 1.00 1318 147 0.1719 0.2509 REMARK 3 4 2.4308 - 2.2085 1.00 1315 146 0.1510 0.2181 REMARK 3 5 2.2085 - 2.0503 0.98 1281 142 0.1559 0.2433 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.890 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 : 0.007 879 REMARK 3 ANGLE : 0.990 1182 REMARK 3 CHIRALITY : 0.033 132 REMARK 3 PLANARITY : 0.004 154 REMARK 3 DIHEDRAL : 13.693 328 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 5KQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000221116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-16 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7521 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.13100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 17.39 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: 2E7P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CH3COONA PH=4.5 20%-24% PEG3350 REMARK 280 (W/V), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-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 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 21.50550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.14950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.50550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.14950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 -7 REMARK 465 SER A -6 REMARK 465 THR A -5 REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 VAL A 4 REMARK 465 LEU A 5 REMARK 465 SER A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 GLN A 9 REMARK 465 ILE A 120 REMARK 465 GLU A 121 REMARK 465 SER A 122 REMARK 465 THR A 123 REMARK 465 ALA A 124 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH A 201 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT REMARK 999 KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. REMARK 999 AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KX517761 FOR REMARK 999 THIS SEQUENCE. THE CONSTRUCT WAS EXPRESSED WITH THE EXPRESSION GST REMARK 999 TAG. DBREF 5KQA A -7 124 PDB 5KQA 5KQA -7 124 SEQRES 1 A 132 GLY SER THR GLY PRO LEU GLY SER MET GLY SER VAL LEU SEQRES 2 A 132 SER SER GLY GLN PRO THR GLU GLU GLN LEU LYS MET ALA SEQRES 3 A 132 LEU GLN LYS ALA GLN GLN LEU VAL ASN SER ASN PRO LEU SEQRES 4 A 132 VAL VAL PHE SER LYS THR TYR CYS GLY TYR CYS SER ARG SEQRES 5 A 132 VAL LYS LYS LEU PHE ASP GLN LEU GLY ALA ARG TYR GLN SEQRES 6 A 132 THR ILE GLU LEU ASP GLN GLU SER ASP GLY ASP ALA ILE SEQRES 7 A 132 GLN ALA ALA LEU LEU GLN TRP THR GLY GLN ARG THR VAL SEQRES 8 A 132 PRO ASN VAL PHE ILE GLY GLY LYS HIS ILE GLY GLY CYS SEQRES 9 A 132 ASP SER VAL MET GLU LYS HIS ARG ASP GLY LYS LEU VAL SEQRES 10 A 132 PRO MET LEU THR GLU CYS GLY ALA ILE ALA ILE GLU SER SEQRES 11 A 132 THR ALA HET GSH A 201 35 HETNAM GSH GLUTATHIONE FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 HOH *95(H2 O) HELIX 1 AA1 THR A 11 SER A 28 1 18 HELIX 2 AA2 CYS A 39 GLY A 53 1 15 HELIX 3 AA3 ASP A 62 GLU A 64 5 3 HELIX 4 AA4 ASP A 66 GLY A 79 1 14 HELIX 5 AA5 GLY A 95 ASP A 105 1 11 HELIX 6 AA6 LYS A 107 CYS A 115 1 9 SHEET 1 AA1 4 GLN A 57 GLU A 60 0 SHEET 2 AA1 4 LEU A 31 SER A 35 1 N SER A 35 O ILE A 59 SHEET 3 AA1 4 ASN A 85 ILE A 88 -1 O PHE A 87 N VAL A 32 SHEET 4 AA1 4 LYS A 91 GLY A 94 -1 O ILE A 93 N VAL A 86 CISPEP 1 VAL A 83 PRO A 84 0 2.14 SITE 1 AC1 14 ASN A 27 LYS A 36 CYS A 39 TYR A 41 SITE 2 AC1 14 GLN A 71 THR A 82 VAL A 83 PRO A 84 SITE 3 AC1 14 GLY A 95 CYS A 96 ASP A 97 HOH A 301 SITE 4 AC1 14 HOH A 303 HOH A 327 CRYST1 43.011 92.299 28.133 90.00 90.00 90.00 P 21 21 2 4 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 0.023250 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035545 0.00000