HEADER OXIDOREDUCTASE 25-NOV-20 7DKR TITLE CRYSTAL STRUCTURE OF NATIVE E. COLI GRX2 AT 2.38 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUTAREDOXIN 2 (GRX2),GLUTAREDOXIN GLUTAREDOXIN, COMPND 5 GLUTAREDOXIN,GRXB FAMILY,GLUTAREDOXIN-2,GLUTAREDOXIN-2 GRX2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS OXIDOREDUCTASE, E. COLI GRX2, NATIVE EXPDTA X-RAY DIFFRACTION AUTHOR S.N.SREEKUMAR,A.AROCKIASAMY REVDAT 2 29-NOV-23 7DKR 1 REMARK REVDAT 1 08-DEC-21 7DKR 0 JRNL AUTH S.N.SREEKUMAR,A.AROCKIASAMY JRNL TITL CRYSTAL STRUCTURE OF NATIVE E. COLI GRX2 AT 2.38 A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 8601 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 396 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 3.4292 - 2.7221 1.00 2699 133 0.2151 0.2784 REMARK 3 2 2.7221 - 2.3780 1.00 2660 125 0.2161 0.2992 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.58 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7DKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300018708. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-20 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8647 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.380 REMARK 200 RESOLUTION RANGE LOW (A) : 89.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4KX4 REMARK 200 REMARK 200 REMARK: 2D CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 25MG/ML IN 25MM TRIS REMARK 280 PH 8.0, 150 MM NACL, RESERVOIR CONDITION:0.1M HEPES PH:7.5, 20% REMARK 280 W/V PEG 10000, PROTEIN/RESERVOIR MIXED IN 1:1, 1:2 AND 2:1 RATIO, REMARK 280 SET UP USING MRC SWISSCI 3 WELL PLATES WITH THE DROP SIZE OF REMARK 280 150 NL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K 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 14.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.64000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.47500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.64000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.47500 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 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 61 125.46 71.36 REMARK 500 TYR A 96 -11.90 -146.54 REMARK 500 ALA A 163 119.22 -170.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DKR A 1 215 UNP C3TEC2 C3TEC2_ECOLX 1 215 SEQRES 1 A 215 MET LYS LEU TYR ILE TYR ASP HIS CYS PRO TYR CYS LEU SEQRES 2 A 215 LYS ALA ARG MET ILE PHE GLY LEU LYS ASN ILE PRO VAL SEQRES 3 A 215 GLU LEU HIS VAL LEU LEU ASN ASP ASP ALA GLU THR PRO SEQRES 4 A 215 THR ARG MET VAL GLY GLN LYS GLN VAL PRO ILE LEU GLN SEQRES 5 A 215 LYS ASP ASP SER ARG TYR MET PRO GLU SER MET ASP ILE SEQRES 6 A 215 VAL HIS TYR VAL ASP LYS LEU ASP GLY LYS PRO LEU LEU SEQRES 7 A 215 THR GLY LYS ARG SER PRO ALA ILE GLU GLU TRP LEU ARG SEQRES 8 A 215 LYS VAL ASN GLY TYR ALA ASN LYS LEU LEU LEU PRO ARG SEQRES 9 A 215 PHE ALA LYS SER ALA PHE ASP GLU PHE SER THR PRO ALA SEQRES 10 A 215 ALA ARG LYS TYR PHE VAL ASP LYS LYS GLU ALA SER ALA SEQRES 11 A 215 GLY ASN PHE ALA ASP LEU LEU ALA HIS SER ASP GLY LEU SEQRES 12 A 215 ILE LYS ASN ILE SER ASP ASP LEU ARG ALA LEU ASP LYS SEQRES 13 A 215 LEU ILE VAL LYS PRO ASN ALA VAL ASN GLY GLU LEU SER SEQRES 14 A 215 GLU ASP ASP ILE GLN LEU PHE PRO LEU LEU ARG ASN LEU SEQRES 15 A 215 THR LEU VAL ALA GLY ILE ASN TRP PRO SER ARG VAL ALA SEQRES 16 A 215 ASP TYR ARG ASP ASN MET ALA LYS GLN THR GLN ILE ASN SEQRES 17 A 215 LEU LEU SER SER MET ALA ILE HELIX 1 AA1 CYS A 9 LYS A 22 1 14 HELIX 2 AA2 ALA A 36 GLY A 44 1 9 HELIX 3 AA3 GLU A 61 LEU A 72 1 12 HELIX 4 AA4 SER A 83 ASN A 94 1 12 HELIX 5 AA5 TYR A 96 ALA A 106 1 11 HELIX 6 AA6 PHE A 110 SER A 114 5 5 HELIX 7 AA7 THR A 115 GLU A 127 1 13 HELIX 8 AA8 GLY A 131 HIS A 139 1 9 HELIX 9 AA9 HIS A 139 LYS A 156 1 18 HELIX 10 AB1 SER A 169 THR A 183 1 15 HELIX 11 AB2 PRO A 191 GLN A 206 1 16 HELIX 12 AB3 LEU A 210 ALA A 214 5 5 SHEET 1 AA1 4 GLU A 27 VAL A 30 0 SHEET 2 AA1 4 LYS A 2 ILE A 5 1 N LEU A 3 O HIS A 29 SHEET 3 AA1 4 ILE A 50 GLN A 52 -1 O GLN A 52 N LYS A 2 SHEET 4 AA1 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 5.33 CRYST1 28.470 78.950 89.280 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 0.035125 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012666 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011201 0.00000