HEADER ELECTRON TRANSPORT 17-MAY-13 4KSM TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI GLUTRAREDOXIN 2 C9S/C12S MUTANT TITLE 2 WITHOUT GLUTATHIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GRX2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GRXB, B1064, JW1051; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTAREDOXIN, GLUTATHIONE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.YE,S.VENKADESH,B.P.ROSEN REVDAT 2 28-FEB-24 4KSM 1 REMARK SEQADV REVDAT 1 21-MAY-14 4KSM 0 JRNL AUTH J.YE,S.VENKADESH,B.P.ROSEN JRNL TITL CRYSTAL STRUCTURES OF E.COLI GLUTAREDOXIN 2 WITH GLUTATHIONE JRNL TITL 2 AND OF A MUTANT C9S/C12S WITHOUT GLUTATHIONE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 8125 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.650 REMARK 3 FREE R VALUE TEST SET COUNT : 378 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 29.4930 - 3.4604 0.97 2652 130 0.2013 0.2712 REMARK 3 2 3.4604 - 2.7472 0.99 2567 126 0.2327 0.3285 REMARK 3 3 2.7472 - 2.4001 0.99 2528 122 0.1770 0.2804 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.70 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 1770 REMARK 3 ANGLE : 1.176 2395 REMARK 3 CHIRALITY : 0.081 267 REMARK 3 PLANARITY : 0.005 309 REMARK 3 DIHEDRAL : 14.076 682 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 4KSM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000079743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 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 FR-D REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8139 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 0.2 M AMMONIUM REMARK 280 ACETATE AND 30% PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.08000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.58000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.58000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.08000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.32500 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 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 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 GLU A 61 105.20 74.05 REMARK 500 TYR A 96 -21.46 -145.90 REMARK 500 ALA A 163 113.42 -169.69 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 TRS A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KX4 RELATED DB: PDB DBREF 4KSM A 1 215 UNP P0AC59 GLRX2_ECOLI 1 215 SEQADV 4KSM ALA A -1 UNP P0AC59 EXPRESSION TAG SEQADV 4KSM SER A 9 UNP P0AC59 CYS 9 ENGINEERED MUTATION SEQADV 4KSM SER A 12 UNP P0AC59 CYS 12 ENGINEERED MUTATION SEQRES 1 A 216 ALA MET LYS LEU TYR ILE TYR ASP HIS SER PRO TYR SER SEQRES 2 A 216 LEU LYS ALA ARG MET ILE PHE GLY LEU LYS ASN ILE PRO SEQRES 3 A 216 VAL GLU LEU HIS VAL LEU LEU ASN ASP ASP ALA GLU THR SEQRES 4 A 216 PRO THR ARG MET VAL GLY GLN LYS GLN VAL PRO ILE LEU SEQRES 5 A 216 GLN LYS ASP ASP SER ARG TYR MET PRO GLU SER MET ASP SEQRES 6 A 216 ILE VAL HIS TYR VAL ASP LYS LEU ASP GLY LYS PRO LEU SEQRES 7 A 216 LEU THR GLY LYS ARG SER PRO ALA ILE GLU GLU TRP LEU SEQRES 8 A 216 ARG LYS VAL ASN GLY TYR ALA ASN LYS LEU LEU LEU PRO SEQRES 9 A 216 ARG PHE ALA LYS SER ALA PHE ASP GLU PHE SER THR PRO SEQRES 10 A 216 ALA ALA ARG LYS TYR PHE VAL ASP LYS LYS GLU ALA SER SEQRES 11 A 216 ALA GLY ASN PHE ALA ASP LEU LEU ALA HIS SER ASP GLY SEQRES 12 A 216 LEU ILE LYS ASN ILE SER ASP ASP LEU ARG ALA LEU ASP SEQRES 13 A 216 LYS LEU ILE VAL LYS PRO ASN ALA VAL ASN GLY GLU LEU SEQRES 14 A 216 SER GLU ASP ASP ILE GLN LEU PHE PRO LEU LEU ARG ASN SEQRES 15 A 216 LEU THR LEU VAL ALA GLY ILE ASN TRP PRO SER ARG VAL SEQRES 16 A 216 ALA ASP TYR ARG ASP ASN MET ALA LYS GLN THR GLN ILE SEQRES 17 A 216 ASN LEU LEU SER SER MET ALA ILE HET TRS A 301 8 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 HOH *74(H2 O) HELIX 1 1 SER A 9 LYS A 22 1 14 HELIX 2 2 ALA A 36 GLY A 44 1 9 HELIX 3 3 GLU A 61 LYS A 71 1 11 HELIX 4 4 SER A 83 ASN A 94 1 12 HELIX 5 5 TYR A 96 LYS A 107 1 12 HELIX 6 6 PHE A 110 SER A 114 5 5 HELIX 7 7 THR A 115 GLU A 127 1 13 HELIX 8 8 GLY A 131 HIS A 139 1 9 HELIX 9 9 HIS A 139 LYS A 156 1 18 HELIX 10 10 SER A 169 LEU A 182 1 14 HELIX 11 11 THR A 183 VAL A 185 5 3 HELIX 12 12 PRO A 191 GLN A 206 1 16 HELIX 13 13 LEU A 210 ALA A 214 5 5 SHEET 1 A 4 GLU A 27 VAL A 30 0 SHEET 2 A 4 LYS A 2 ILE A 5 1 N LEU A 3 O HIS A 29 SHEET 3 A 4 ILE A 50 GLN A 52 -1 O ILE A 50 N TYR A 4 SHEET 4 A 4 TYR A 58 MET A 59 -1 O MET A 59 N LEU A 51 CISPEP 1 VAL A 48 PRO A 49 0 5.67 SITE 1 AC1 5 HIS A 8 SER A 9 PRO A 10 LYS A 126 SITE 2 AC1 5 HOH A 413 CRYST1 28.160 78.650 89.160 90.00 90.00 90.00 P 21 21 21 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 0.035511 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011216 0.00000