PDB Short entry for 3QMX HEADER ELECTRON TRANSPORT 05-FEB-11 3QMX TITLE X-RAY CRYSTAL STRUCTURE OF SYNECHOCYSTIS SP. PCC 6803 GLUTAREDOXIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAREDOXIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-88; COMPND 5 SYNONYM: GLUTAREDOXIN 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP.; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 STRAIN: ATCC 27184 / PCC 6803 / N-1; SOURCE 5 GENE: SSR2061; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUTAREDOXIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR R.B.SUTTON,D.B.KNAFF REVDAT 2 13-SEP-23 3QMX 1 REMARK SEQADV REVDAT 1 11-JAN-12 3QMX 0 JRNL AUTH S.G.KIM,J.S.CHUNG,R.B.SUTTON,J.S.LEE,L.LOPEZ-MAURY,S.Y.LEE, JRNL AUTH 2 F.J.FLORENCIO,T.LIN,M.ZABET-MOGHADDAM,M.J.WOOD,K.NAYAK, JRNL AUTH 3 V.MADEM,J.N.TRIPATHY,S.K.KIM,D.B.KNAFF JRNL TITL REDOX, MUTAGENIC AND STRUCTURAL STUDIES OF THE JRNL TITL 2 GLUTAREDOXIN/ARSENATE REDUCTASE COUPLE FROM THE JRNL TITL 3 CYANOBACTERIUM SYNECHOCYSTIS SP. PCC 6803. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1824 392 2011 JRNL REFN ISSN 0006-3002 JRNL PMID 22155275 JRNL DOI 10.1016/J.BBAPAP.2011.10.012 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 6592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.830 REMARK 3 FREE R VALUE TEST SET COUNT : 648 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 30.0639 - 3.1150 0.95 1281 132 0.1672 0.1795 REMARK 3 2 3.1150 - 2.4728 1.00 1267 134 0.1612 0.2016 REMARK 3 3 2.4728 - 2.1603 0.86 1077 130 0.1504 0.1815 REMARK 3 4 2.1603 - 1.9629 1.00 1231 134 0.1537 0.2202 REMARK 3 5 1.9629 - 1.8222 0.87 1088 118 0.1888 0.2338 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 28.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -3.95320 REMARK 3 B22 (A**2) : 5.12890 REMARK 3 B33 (A**2) : -1.17570 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 808 REMARK 3 ANGLE : 0.952 1090 REMARK 3 CHIRALITY : 0.073 111 REMARK 3 PLANARITY : 0.003 143 REMARK 3 DIHEDRAL : 11.909 293 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 3QMX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.822 REMARK 200 RESOLUTION RANGE LOW (A) : 30.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 3GRX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1% PEG 4000, 0.1M HEPES, 1.25M REMARK 280 AMMONIUM SULFATE, PH 8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 18.63900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.41350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.56200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.41350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.63900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.56200 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: 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 O HOH A 140 O HOH A 146 2.09 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 HIS A -3 48.40 -166.58 REMARK 500 ASP A 38 121.57 -39.40 REMARK 500 ALA A 51 36.60 -98.45 REMARK 500 ASP A 64 -1.29 76.65 REMARK 500 HIS A 87 58.76 -117.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 11 TRP A 12 148.08 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 SO4 A 89 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 90 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MSZ RELATED DB: PDB REMARK 900 GLUTAREDOXIN 1 FROM FRANCISELLA TULARENSIS DBREF 3QMX A 2 88 UNP P73492 GLRX2_SYNY3 2 88 SEQADV 3QMX MET A -10 UNP P73492 EXPRESSION TAG SEQADV 3QMX ARG A -9 UNP P73492 EXPRESSION TAG SEQADV 3QMX GLY A -8 UNP P73492 EXPRESSION TAG SEQADV 3QMX SER A -7 UNP P73492 EXPRESSION TAG SEQADV 3QMX HIS A -6 UNP P73492 EXPRESSION TAG SEQADV 3QMX HIS A -5 UNP P73492 EXPRESSION TAG SEQADV 3QMX HIS A -4 UNP P73492 EXPRESSION TAG SEQADV 3QMX HIS A -3 UNP P73492 EXPRESSION TAG SEQADV 3QMX HIS A -2 UNP P73492 EXPRESSION TAG SEQADV 3QMX HIS A -1 UNP P73492 EXPRESSION TAG SEQADV 3QMX GLY A 0 UNP P73492 EXPRESSION TAG SEQADV 3QMX SER A 1 UNP P73492 EXPRESSION TAG SEQRES 1 A 99 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA SEQRES 2 A 99 VAL SER ALA LYS ILE GLU ILE TYR THR TRP SER THR CYS SEQRES 3 A 99 PRO PHE CYS MET ARG ALA LEU ALA LEU LEU LYS ARG LYS SEQRES 4 A 99 GLY VAL GLU PHE GLN GLU TYR CYS ILE ASP GLY ASP ASN SEQRES 5 A 99 GLU ALA ARG GLU ALA MET ALA ALA ARG ALA ASN GLY LYS SEQRES 6 A 99 ARG SER LEU PRO GLN ILE PHE ILE ASP ASP GLN HIS ILE SEQRES 7 A 99 GLY GLY CYS ASP ASP ILE TYR ALA LEU ASP GLY ALA GLY SEQRES 8 A 99 LYS LEU ASP PRO LEU LEU HIS SER HET SO4 A 89 5 HET SO4 A 90 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *74(H2 O) HELIX 1 1 CYS A 15 GLY A 29 1 15 HELIX 2 2 ASP A 40 ALA A 51 1 12 HELIX 3 3 GLY A 69 ALA A 79 1 11 HELIX 4 4 LYS A 81 LEU A 86 1 6 SHEET 1 A 4 GLN A 33 CYS A 36 0 SHEET 2 A 4 ILE A 7 THR A 11 1 N ILE A 9 O TYR A 35 SHEET 3 A 4 GLN A 59 ILE A 62 -1 O PHE A 61 N GLU A 8 SHEET 4 A 4 GLN A 65 GLY A 68 -1 O ILE A 67 N ILE A 60 CISPEP 1 LEU A 57 PRO A 58 0 -3.10 CISPEP 2 LEU A 86 HIS A 87 0 2.95 SITE 1 AC1 11 HIS A -1 HIS A -4 HIS A -3 HIS A -2 SITE 2 AC1 11 GLY A 0 GLY A 78 HOH A 106 HOH A 113 SITE 3 AC1 11 HOH A 114 HOH A 119 HOH A 139 SITE 1 AC2 8 PHE A 17 LEU A 57 PRO A 58 CYS A 70 SITE 2 AC2 8 ASP A 71 HOH A 98 HOH A 118 HOH A 159 CRYST1 37.278 39.124 50.827 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 0.026825 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019675 0.00000