HEADER PLANT PROTEIN 19-AUG-15 5D9W TITLE DEHYDROASCORBATE REDUCTASE (OSDHAR) COMPLEXED WITH ASA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHYDROASCORBATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OS05G0116100 PROTEIN,CDNA CLONE:001-040-D08,FULL INSERT COMPND 5 SEQUENCE,CDNA CLONE:J023074C02; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA SUBSP. JAPONICA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: P0496H07.8, OS05G0116100, OJ1654_B10.18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: NICO21(DE3) KEYWDS OSDHAR, ORYZA SATIVA L. JAPONICA, ASCORBATE, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.DO,J.H.LEE REVDAT 3 20-MAR-24 5D9W 1 HETSYN REVDAT 2 29-JUL-20 5D9W 1 REMARK SITE REVDAT 1 03-FEB-16 5D9W 0 JRNL AUTH H.DO,I.S.KIM,B.W.JEON,C.W.LEE,A.K.PARK,A.R.WI,S.C.SHIN, JRNL AUTH 2 H.PARK,Y.S.KIM,H.S.YOON,H.W.KIM,J.H.LEE JRNL TITL STRUCTURAL UNDERSTANDING OF THE RECYCLING OF OXIDIZED JRNL TITL 2 ASCORBATE BY DEHYDROASCORBATE REDUCTASE (OSDHAR) FROM ORYZA JRNL TITL 3 SATIVA L. JAPONICA JRNL REF SCI REP V. 6 19498 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 26775680 JRNL DOI 10.1038/SREP19498 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 23319 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1097 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 28.6152 - 3.3777 0.97 2848 118 0.1599 0.1704 REMARK 3 2 3.3777 - 2.6817 0.99 2846 147 0.2233 0.2767 REMARK 3 3 2.6817 - 2.3429 0.99 2810 137 0.2365 0.2676 REMARK 3 4 2.3429 - 2.1287 0.99 2773 167 0.2287 0.2727 REMARK 3 5 2.1287 - 1.9762 0.98 2796 138 0.2199 0.2517 REMARK 3 6 1.9762 - 1.8597 0.98 2795 127 0.2424 0.2942 REMARK 3 7 1.8597 - 1.7666 0.98 2758 144 0.2516 0.2826 REMARK 3 8 1.7666 - 1.6897 0.93 2596 119 0.2754 0.3154 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.170 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 1708 REMARK 3 ANGLE : 0.908 2323 REMARK 3 CHIRALITY : 0.036 259 REMARK 3 PLANARITY : 0.004 296 REMARK 3 DIHEDRAL : 12.323 626 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): 10.1829 -0.5841 8.8692 REMARK 3 T TENSOR REMARK 3 T11: 0.2439 T22: 0.1886 REMARK 3 T33: 0.2233 T12: 0.0229 REMARK 3 T13: -0.0491 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 2.7579 L22: 3.7175 REMARK 3 L33: 2.0195 L12: -0.7720 REMARK 3 L13: 0.0067 L23: -0.5514 REMARK 3 S TENSOR REMARK 3 S11: -0.2201 S12: -0.3159 S13: 0.0913 REMARK 3 S21: 0.4994 S22: 0.1267 S23: -0.4033 REMARK 3 S31: -0.1210 S32: -0.0250 S33: 0.0722 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 5D9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1-6.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.8000 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 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS HCL, PH 6.6, 28%(W/V) REMARK 280 PEG3350, 10MM CACL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.63950 REMARK 290 SMTRY3 2 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 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 MET A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 ALA A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 213 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 ASN A 46 62.55 -156.91 REMARK 500 ASP A 67 27.27 -74.85 REMARK 500 LYS A 69 141.35 -176.03 REMARK 500 ASP A 73 102.99 79.60 REMARK 500 ASN A 143 53.23 -108.66 REMARK 500 ASN A 146 -145.75 -113.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D9T RELATED DB: PDB REMARK 900 RELATED ID: 5D9V RELATED DB: PDB REMARK 900 RELATED ID: 5D9X RELATED DB: PDB DBREF 5D9W A 1 213 UNP Q65XA0 Q65XA0_ORYSJ 1 213 SEQADV 5D9W MET A -16 UNP Q65XA0 INITIATING METHIONINE SEQADV 5D9W HIS A -15 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W HIS A -14 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W HIS A -13 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W HIS A -12 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W HIS A -11 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W HIS A -10 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W ALA A -9 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W SER A -8 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W GLU A -7 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W ASN A -6 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W LEU A -5 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W TYR A -4 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W PHE A -3 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W GLN A -2 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W GLY A -1 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W ALA A 0 UNP Q65XA0 EXPRESSION TAG SEQADV 5D9W SER A 20 UNP Q65XA0 CYS 20 ENGINEERED MUTATION SEQRES 1 A 230 MET HIS HIS HIS HIS HIS HIS ALA SER GLU ASN LEU TYR SEQRES 2 A 230 PHE GLN GLY ALA MET GLY VAL GLU VAL CYS VAL LYS ALA SEQRES 3 A 230 ALA VAL GLY HIS PRO ASP THR LEU GLY ASP SER PRO PHE SEQRES 4 A 230 SER GLN ARG VAL LEU LEU THR LEU GLU GLU LYS LYS VAL SEQRES 5 A 230 PRO TYR GLU MET LYS LEU ILE ASP VAL GLN ASN LYS PRO SEQRES 6 A 230 ASP TRP PHE LEU LYS ILE SER PRO GLU GLY LYS VAL PRO SEQRES 7 A 230 VAL PHE ASN GLY GLY ASP GLY LYS TRP ILE PRO ASP SER SEQRES 8 A 230 ASP VAL ILE THR GLN VAL ILE GLU GLU LYS TYR PRO THR SEQRES 9 A 230 PRO SER LEU VAL THR PRO PRO GLU TYR ALA SER VAL GLY SEQRES 10 A 230 SER LYS ILE PHE SER CYS PHE THR THR PHE LEU LYS SER SEQRES 11 A 230 LYS ASP PRO ASN ASP GLY SER GLU LYS ALA LEU LEU THR SEQRES 12 A 230 GLU LEU GLN ALA LEU GLU GLU HIS LEU LYS ALA HIS GLY SEQRES 13 A 230 PRO PHE ILE ASN GLY GLN ASN ILE SER ALA ALA ASP LEU SEQRES 14 A 230 SER LEU ALA PRO LYS LEU TYR HIS LEU GLN VAL ALA LEU SEQRES 15 A 230 GLU HIS PHE LYS GLY TRP LYS ILE PRO GLU ASP LEU THR SEQRES 16 A 230 ASN VAL HIS ALA TYR THR GLU ALA LEU PHE SER ARG GLU SEQRES 17 A 230 SER PHE ILE LYS THR LYS ALA ALA LYS GLU HIS LEU ILE SEQRES 18 A 230 ALA GLY TRP ALA PRO LYS VAL ASN ALA HET ASC A 301 20 HETNAM ASC ASCORBIC ACID HETSYN ASC VITAMIN C FORMUL 2 ASC C6 H8 O6 FORMUL 3 HOH *37(H2 O) HELIX 1 AA1 SER A 20 LYS A 33 1 14 HELIX 2 AA2 PRO A 48 SER A 55 1 8 HELIX 3 AA3 ASP A 73 TYR A 85 1 13 HELIX 4 AA4 PRO A 93 ALA A 97 5 5 HELIX 5 AA5 LYS A 102 SER A 113 1 12 HELIX 6 AA6 GLY A 119 GLY A 139 1 21 HELIX 7 AA7 SER A 148 GLY A 170 1 23 HELIX 8 AA8 LEU A 177 SER A 189 1 13 HELIX 9 AA9 ARG A 190 LYS A 197 1 8 HELIX 10 AB1 ALA A 199 ASN A 212 1 14 SHEET 1 AA1 3 HIS A 13 LEU A 17 0 SHEET 2 AA1 3 VAL A 3 ALA A 10 -1 N ALA A 10 O THR A 16 SHEET 3 AA1 3 TYR A 37 ILE A 42 1 O LYS A 40 N VAL A 5 SHEET 1 AA2 4 HIS A 13 LEU A 17 0 SHEET 2 AA2 4 VAL A 3 ALA A 10 -1 N ALA A 10 O THR A 16 SHEET 3 AA2 4 VAL A 62 ASN A 64 -1 O ASN A 64 N GLU A 4 SHEET 4 AA2 4 TRP A 70 PRO A 72 -1 O ILE A 71 N PHE A 63 CISPEP 1 VAL A 60 PRO A 61 0 3.81 CISPEP 2 THR A 87 PRO A 88 0 2.76 CISPEP 3 GLY A 139 PRO A 140 0 1.49 CISPEP 4 GLN A 145 ASN A 146 0 7.21 CRYST1 46.848 47.279 50.992 90.00 108.23 90.00 P 1 21 1 2 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 0.021346 0.000000 0.007029 0.00000 SCALE2 0.000000 0.021151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020647 0.00000