HEADER OXIDOREDUCTASE 11-APR-17 5XFT TITLE CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII DEHYDROASCORBATE TITLE 2 REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHYDROASCORBATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 5-218; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYDOMONAS REINHARDTII; SOURCE 3 ORGANISM_TAXID: 3055; SOURCE 4 GENE: CHLREDRAFT_143082; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHLAMYDOMONAS, DEHYDROGENASE REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.Y.CHANG,T.P.KO,K.F.HUANG REVDAT 2 22-NOV-23 5XFT 1 JRNL REVDAT 1 27-DEC-17 5XFT 0 JRNL AUTH H.Y.CHANG,S.T.LIN,T.P.KO,S.M.WU,T.H.LIN,Y.C.CHANG,K.F.HUANG, JRNL AUTH 2 T.M.LEE JRNL TITL ENZYMATIC CHARACTERIZATION AND CRYSTAL STRUCTURE ANALYSIS OF JRNL TITL 2 CHLAMYDOMONAS REINHARDTII DEHYDROASCORBATE REDUCTASE AND JRNL TITL 3 THEIR IMPLICATIONS FOR OXIDATIVE STRESS JRNL REF PLANT PHYSIOL. BIOCHEM. V. 120 144 2017 JRNL REFN ESSN 1873-2690 JRNL PMID 29028546 JRNL DOI 10.1016/J.PLAPHY.2017.09.026 REMARK 2 REMARK 2 RESOLUTION. 2.46 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 8796 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 413 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 0.0000 - 3.5440 1.00 3331 155 0.1703 0.1823 REMARK 3 2 3.5440 - 2.5500 0.96 3021 146 0.2034 0.2780 REMARK 3 3 2.5500 - 2.4600 0.65 2031 112 0.2243 0.2492 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.450 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 : 0.005 1735 REMARK 3 ANGLE : 0.744 2362 REMARK 3 CHIRALITY : 0.045 255 REMARK 3 PLANARITY : 0.006 305 REMARK 3 DIHEDRAL : 15.424 1037 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 28.1982 4.9816 10.1374 REMARK 3 T TENSOR REMARK 3 T11: 0.0055 T22: -0.0140 REMARK 3 T33: -0.1164 T12: 0.0816 REMARK 3 T13: 0.1069 T23: -0.2489 REMARK 3 L TENSOR REMARK 3 L11: 0.0297 L22: 0.1469 REMARK 3 L33: 0.0079 L12: 0.0025 REMARK 3 L13: -0.0125 L23: 0.0197 REMARK 3 S TENSOR REMARK 3 S11: 0.0369 S12: 0.0443 S13: 0.0704 REMARK 3 S21: 0.0104 S22: -0.1122 S23: 0.3173 REMARK 3 S31: 0.0386 S32: -0.0274 S33: -0.0485 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 5XFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-APR-17. REMARK 100 THE DEPOSITION ID IS D_1300003449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9862 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5D9T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 8.0, WITH 2 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 23.82600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.29900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.29900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.91300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.29900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.29900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.73900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.29900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.29900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 11.91300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.29900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.29900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.73900 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 23.82600 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 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 358 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 359 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 459 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 469 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 490 LIES ON A SPECIAL POSITION. 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 LYS A 216 REMARK 465 HIS A 217 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 LEU A 19 -157.63 -108.74 REMARK 500 ASN A 47 61.21 -163.81 REMARK 500 SER A 56 12.35 -150.64 REMARK 500 ASP A 74 112.58 72.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 483 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 484 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 486 DISTANCE = 6.99 ANGSTROMS REMARK 525 HOH A 487 DISTANCE = 7.10 ANGSTROMS REMARK 525 HOH A 488 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A 489 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A 490 DISTANCE = 7.57 ANGSTROMS REMARK 525 HOH A 491 DISTANCE = 7.81 ANGSTROMS REMARK 525 HOH A 492 DISTANCE = 7.93 ANGSTROMS REMARK 525 HOH A 493 DISTANCE = 8.48 ANGSTROMS DBREF 5XFT A 4 217 UNP A8I0K9 A8I0K9_CHLRE 5 218 SEQADV 5XFT SER A 1 UNP A8I0K9 EXPRESSION TAG SEQADV 5XFT ASN A 2 UNP A8I0K9 EXPRESSION TAG SEQADV 5XFT ILE A 3 UNP A8I0K9 EXPRESSION TAG SEQRES 1 A 217 SER ASN ILE VAL THR THR ILE TYR VAL LYS GLY ASP PRO SEQRES 2 A 217 ALA LYS ASN LYS LEU LEU ASP CYS PRO PHE CYS HIS ARG SEQRES 3 A 217 VAL LEU LEU ALA TYR GLU ALA LYS LYS LEU PRO TYR LYS SEQRES 4 A 217 MET GLU TYR ILE ASP PHE ASP ASN LYS PRO ALA TRP LEU SEQRES 5 A 217 LEU GLU ALA SER GLY GLY LYS VAL PRO VAL ILE LYS GLU SEQRES 6 A 217 GLY PRO ASP ALA PRO TYR MET PRO ASP SER ASP VAL ILE SEQRES 7 A 217 VAL VAL HIS LEU GLU LYS GLN HIS PRO GLU PRO SER LEU SEQRES 8 A 217 GLN SER SER VAL PRO ALA GLU ILE GLY ALA LYS LEU PHE SEQRES 9 A 217 PRO ASN PHE ARG ALA ILE LEU ILE GLY PRO ALA ALA GLU SEQRES 10 A 217 VAL ALA ASP LYS VAL ALA ALA LEU GLU GLU GLN LEU ALA SEQRES 11 A 217 GLY MET ASP ASP TYR LEU ARG GLN HIS GLU ALA GLN GLY SEQRES 12 A 217 PRO LEU PHE GLY GLY GLN HIS LEU ASN GLY THR ASP CYS SEQRES 13 A 217 SER LEU ALA PRO LYS LEU TYR HIS ALA VAL VAL ALA LEU SEQRES 14 A 217 LYS HIS PHE LYS GLY TRP GLU LEU PRO ALA ARG PHE THR SEQRES 15 A 217 ALA LEU HIS LYS TYR LEU ALA ALA LEU LYS ALA LEU PRO SEQRES 16 A 217 GLU TRP GLN HIS VAL ASP TYR GLY THR GLU ALA ILE ILE SEQRES 17 A 217 ALA GLY TRP GLU ARG HIS ILE LYS HIS FORMUL 2 HOH *193(H2 O) HELIX 1 AA1 PRO A 13 ASN A 16 5 4 HELIX 2 AA2 CYS A 21 LYS A 34 1 14 HELIX 3 AA3 PRO A 49 GLY A 57 1 9 HELIX 4 AA4 ASP A 74 HIS A 86 1 13 HELIX 5 AA5 LYS A 102 GLY A 113 1 12 HELIX 6 AA6 PRO A 114 ALA A 116 5 3 HELIX 7 AA7 GLU A 117 HIS A 139 1 23 HELIX 8 AA8 ASN A 152 GLY A 174 1 23 HELIX 9 AA9 PHE A 181 LEU A 194 1 14 HELIX 10 AB1 LEU A 194 VAL A 200 1 7 HELIX 11 AB2 GLY A 203 ARG A 213 1 11 SHEET 1 AA1 3 LYS A 17 LEU A 18 0 SHEET 2 AA1 3 THR A 5 ASP A 12 -1 N ASP A 12 O LYS A 17 SHEET 3 AA1 3 TYR A 38 ILE A 43 1 O ILE A 43 N VAL A 9 SHEET 1 AA2 4 LYS A 17 LEU A 18 0 SHEET 2 AA2 4 THR A 5 ASP A 12 -1 N ASP A 12 O LYS A 17 SHEET 3 AA2 4 VAL A 62 LYS A 64 -1 O VAL A 62 N TYR A 8 SHEET 4 AA2 4 MET A 72 PRO A 73 -1 O MET A 72 N ILE A 63 CISPEP 1 VAL A 60 PRO A 61 0 2.87 CISPEP 2 GLU A 88 PRO A 89 0 -4.39 CRYST1 104.598 104.598 47.652 90.00 90.00 90.00 P 41 21 2 8 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 0.009560 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020985 0.00000