HEADER OXIDOREDUCTASE 23-AUG-16 5GTX TITLE CRYSTAL STRUCTURE OF MUTATED BUCKWHEAT GLUTAREDOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BUCKWHEAT GLUTAREDOXIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POLYGONACEAE; SOURCE 3 ORGANISM_TAXID: 3615; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTAREDOXIN, GLUTATHIONE, ENZYMATIC ACTIVITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,W.WANG,Y.ZHAO,Z.WANG,H.WANG REVDAT 3 08-NOV-23 5GTX 1 REMARK REVDAT 2 27-SEP-17 5GTX 1 REMARK REVDAT 1 05-JUL-17 5GTX 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. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 551 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 40.4537 - 3.6322 1.00 2748 142 0.1859 0.2139 REMARK 3 2 3.6322 - 2.8832 1.00 2617 148 0.2247 0.2488 REMARK 3 3 2.8832 - 2.5188 1.00 2590 132 0.2690 0.3322 REMARK 3 4 2.5188 - 2.2800 0.97 2518 129 0.2570 0.2575 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.840 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 1718 REMARK 3 ANGLE : 0.897 2314 REMARK 3 CHIRALITY : 0.050 260 REMARK 3 PLANARITY : 0.006 300 REMARK 3 DIHEDRAL : 18.554 1046 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 5GTX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-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) : 0.9776 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 : 11059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.670 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.10.1-2155 REMARK 200 STARTING MODEL: 5KQA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM CH3COONA PH4.5 AND 23%(W/V) REMARK 280 PEG3350, LIQUID DIFFUSION, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 71.70350 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 71.70350 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 26.62550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.09250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.62550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.09250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.70350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.62550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.09250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.70350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.62550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 31.09250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 -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 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 SER B 3 REMARK 465 VAL B 4 REMARK 465 LEU B 5 REMARK 465 SER B 6 REMARK 465 SER B 7 REMARK 465 GLY B 8 REMARK 465 GLN B 9 REMARK 465 ILE B 120 REMARK 465 GLU B 121 REMARK 465 SER B 122 REMARK 465 THR B 123 REMARK 465 ALA B 124 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 OE1 GLU B 101 NH1 ARG B 104 2.00 REMARK 500 NZ LYS A 47 O HOH A 201 2.04 REMARK 500 N PRO B 10 OE1 GLN B 14 2.12 REMARK 500 OG1 THR A 37 OD2 ASP A 62 2.16 REMARK 500 O ARG B 104 O HOH B 201 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 THR B 11 -136.65 49.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KX517761 FOR REMARK 999 THIS SEQUENCE. DBREF 5GTX A -4 124 PDB 5GTX 5GTX -4 124 DBREF 5GTX B -4 124 PDB 5GTX 5GTX -4 124 SEQRES 1 A 129 GLY PRO LEU GLY SER MET GLY SER VAL LEU SER SER GLY SEQRES 2 A 129 GLN PRO THR GLU GLU GLN LEU LYS MET ALA LEU GLN LYS SEQRES 3 A 129 ALA GLN GLN LEU VAL ASN SER ASN PRO LEU VAL VAL PHE SEQRES 4 A 129 SER LYS THR TYR ALA GLY TYR CYS SER ARG VAL LYS LYS SEQRES 5 A 129 LEU PHE ASP GLN LEU GLY ALA ARG TYR GLN THR ILE GLU SEQRES 6 A 129 LEU ASP GLN GLU SER ASP GLY ASP ALA ILE GLN ALA ALA SEQRES 7 A 129 LEU LEU GLN TRP THR GLY GLN ARG THR VAL PRO ASN VAL SEQRES 8 A 129 PHE ILE GLY GLY LYS HIS ILE GLY GLY CYS ASP SER VAL SEQRES 9 A 129 MET GLU LYS HIS ARG ASP GLY LYS LEU VAL PRO MET LEU SEQRES 10 A 129 THR GLU CYS GLY ALA ILE ALA ILE GLU SER THR ALA SEQRES 1 B 129 GLY PRO LEU GLY SER MET GLY SER VAL LEU SER SER GLY SEQRES 2 B 129 GLN PRO THR GLU GLU GLN LEU LYS MET ALA LEU GLN LYS SEQRES 3 B 129 ALA GLN GLN LEU VAL ASN SER ASN PRO LEU VAL VAL PHE SEQRES 4 B 129 SER LYS THR TYR ALA GLY TYR CYS SER ARG VAL LYS LYS SEQRES 5 B 129 LEU PHE ASP GLN LEU GLY ALA ARG TYR GLN THR ILE GLU SEQRES 6 B 129 LEU ASP GLN GLU SER ASP GLY ASP ALA ILE GLN ALA ALA SEQRES 7 B 129 LEU LEU GLN TRP THR GLY GLN ARG THR VAL PRO ASN VAL SEQRES 8 B 129 PHE ILE GLY GLY LYS HIS ILE GLY GLY CYS ASP SER VAL SEQRES 9 B 129 MET GLU LYS HIS ARG ASP GLY LYS LEU VAL PRO MET LEU SEQRES 10 B 129 THR GLU CYS GLY ALA ILE ALA ILE GLU SER THR ALA FORMUL 3 HOH *27(H2 O) HELIX 1 AA1 THR A 11 ASN A 29 1 19 HELIX 2 AA2 ALA 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 HELIX 7 AA7 GLU B 13 ASN B 29 1 17 HELIX 8 AA8 ALA B 39 LEU B 52 1 14 HELIX 9 AA9 ASP B 62 GLU B 64 5 3 HELIX 10 AB1 ASP B 66 GLY B 79 1 14 HELIX 11 AB2 GLY B 95 ASP B 105 1 11 HELIX 12 AB3 LYS B 107 CYS B 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 GLY A 94 N VAL A 86 SHEET 1 AA2 4 GLN B 57 GLU B 60 0 SHEET 2 AA2 4 LEU B 31 SER B 35 1 N LEU B 31 O GLN B 57 SHEET 3 AA2 4 ASN B 85 ILE B 88 -1 O PHE B 87 N VAL B 32 SHEET 4 AA2 4 LYS B 91 GLY B 94 -1 O ILE B 93 N VAL B 86 CISPEP 1 VAL A 83 PRO A 84 0 -1.34 CISPEP 2 VAL B 83 PRO B 84 0 -0.87 CRYST1 53.251 62.185 143.407 90.00 90.00 90.00 C 2 2 21 16 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 0.018779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006973 0.00000