HEADER ELECTRON TRANSPORT 24-MAY-13 4KX4 TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN 2 COMPLEX WITH TITLE 2 GLUTATHIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GRX2; COMPND 5 ENGINEERED: 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 2, GLUTATHIONE, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.YE,S.VENKADESH,B.P.ROSEN REVDAT 2 28-FEB-24 4KX4 1 REMARK SEQADV REVDAT 1 28-MAY-14 4KX4 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 28634 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 1492 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 22.4712 - 3.5543 0.99 2809 126 0.1505 0.1562 REMARK 3 2 3.5543 - 2.8229 1.00 2674 139 0.1710 0.1841 REMARK 3 3 2.8229 - 2.4666 1.00 2608 150 0.1805 0.2255 REMARK 3 4 2.4666 - 2.2413 1.00 2630 123 0.1653 0.2044 REMARK 3 5 2.2413 - 2.0808 1.00 2547 155 0.1579 0.1878 REMARK 3 6 2.0808 - 1.9582 1.00 2599 150 0.1593 0.2134 REMARK 3 7 1.9582 - 1.8602 1.00 2558 153 0.1723 0.2139 REMARK 3 8 1.8602 - 1.7792 1.00 2568 140 0.1640 0.1935 REMARK 3 9 1.7792 - 1.7107 0.99 2533 141 0.1629 0.1977 REMARK 3 10 1.7107 - 1.6517 0.88 2222 139 0.1610 0.2011 REMARK 3 11 1.6517 - 1.6001 0.54 1394 76 0.1528 0.1924 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.070 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 : 0.006 1778 REMARK 3 ANGLE : 1.235 2403 REMARK 3 CHIRALITY : 0.073 269 REMARK 3 PLANARITY : 0.005 311 REMARK 3 DIHEDRAL : 12.735 678 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 4KX4 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_1000079904. 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) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 32-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 22.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 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 (%): 45.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MM GLUTATHIONE, 20 MM SODIUM REMARK 280 ARSENATE, 100 MM SODIUM CITRATE, 200 MM AMMONIUM ACETATE AND 30 % REMARK 280 PEG 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 101.64667 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 50.82333 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 50.82333 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 101.64667 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 610 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 639 LIES ON A SPECIAL POSITION. 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 ALA A -1 59.09 -147.83 REMARK 500 SER A 56 -2.31 74.35 REMARK 500 GLU A 61 105.46 84.17 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 GSH A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 302 DBREF 4KX4 A 1 215 UNP P0AC59 GLRX2_ECOLI 1 215 SEQADV 4KX4 SER A -2 UNP P0AC59 EXPRESSION TAG SEQADV 4KX4 ALA A -1 UNP P0AC59 EXPRESSION TAG SEQADV 4KX4 ASP A 87 UNP P0AC59 GLU 87 CONFLICT SEQRES 1 A 217 SER ALA MET LYS LEU TYR ILE TYR ASP HIS CYS PRO TYR SEQRES 2 A 217 CYS LEU LYS ALA ARG MET ILE PHE GLY LEU LYS ASN ILE SEQRES 3 A 217 PRO VAL GLU LEU HIS VAL LEU LEU ASN ASP ASP ALA GLU SEQRES 4 A 217 THR PRO THR ARG MET VAL GLY GLN LYS GLN VAL PRO ILE SEQRES 5 A 217 LEU GLN LYS ASP ASP SER ARG TYR MET PRO GLU SER MET SEQRES 6 A 217 ASP ILE VAL HIS TYR VAL ASP LYS LEU ASP GLY LYS PRO SEQRES 7 A 217 LEU LEU THR GLY LYS ARG SER PRO ALA ILE ASP GLU TRP SEQRES 8 A 217 LEU ARG LYS VAL ASN GLY TYR ALA ASN LYS LEU LEU LEU SEQRES 9 A 217 PRO ARG PHE ALA LYS SER ALA PHE ASP GLU PHE SER THR SEQRES 10 A 217 PRO ALA ALA ARG LYS TYR PHE VAL ASP LYS LYS GLU ALA SEQRES 11 A 217 SER ALA GLY ASN PHE ALA ASP LEU LEU ALA HIS SER ASP SEQRES 12 A 217 GLY LEU ILE LYS ASN ILE SER ASP ASP LEU ARG ALA LEU SEQRES 13 A 217 ASP LYS LEU ILE VAL LYS PRO ASN ALA VAL ASN GLY GLU SEQRES 14 A 217 LEU SER GLU ASP ASP ILE GLN LEU PHE PRO LEU LEU ARG SEQRES 15 A 217 ASN LEU THR LEU VAL ALA GLY ILE ASN TRP PRO SER ARG SEQRES 16 A 217 VAL ALA ASP TYR ARG ASP ASN MET ALA LYS GLN THR GLN SEQRES 17 A 217 ILE ASN LEU LEU SER SER MET ALA ILE HET GSH A 301 20 HET ACY A 302 4 HETNAM GSH GLUTATHIONE HETNAM ACY ACETIC ACID FORMUL 2 GSH C10 H17 N3 O6 S FORMUL 3 ACY C2 H4 O2 FORMUL 4 HOH *301(H2 O) HELIX 1 1 CYS A 9 LYS A 22 1 14 HELIX 2 2 ALA A 36 GLY A 44 1 9 HELIX 3 3 GLU A 61 LEU A 72 1 12 HELIX 4 4 SER A 83 GLY A 95 1 13 HELIX 5 5 ALA A 97 ALA A 106 1 10 HELIX 6 6 PHE A 110 SER A 114 5 5 HELIX 7 7 THR A 115 GLY A 131 1 17 HELIX 8 8 ASN A 132 HIS A 139 1 8 HELIX 9 9 HIS A 139 LYS A 156 1 18 HELIX 10 10 SER A 169 THR A 183 1 15 HELIX 11 11 PRO A 191 GLN A 206 1 16 HELIX 12 12 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 GLU A 27 SHEET 3 A 4 ILE A 50 GLN A 52 -1 O GLN A 52 N LYS A 2 SHEET 4 A 4 TYR A 58 PRO A 60 -1 O MET A 59 N LEU A 51 CISPEP 1 VAL A 48 PRO A 49 0 2.55 SITE 1 AC1 20 TYR A 6 CYS A 9 TYR A 11 LYS A 46 SITE 2 AC1 20 GLN A 47 VAL A 48 PRO A 49 GLU A 61 SITE 3 AC1 20 SER A 62 PRO A 84 LYS A 125 HOH A 401 SITE 4 AC1 20 HOH A 402 HOH A 420 HOH A 444 HOH A 456 SITE 5 AC1 20 HOH A 482 HOH A 501 HOH A 615 HOH A 644 SITE 1 AC2 6 PRO A 10 ARG A 91 ASN A 98 HOH A 504 SITE 2 AC2 6 HOH A 509 HOH A 681 CRYST1 50.100 50.100 152.470 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 0.019960 0.011524 0.000000 0.00000 SCALE2 0.000000 0.023048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006559 0.00000