HEADER OXIDOREDUCTASE 10-OCT-98 1BX1 TITLE FERREDOXIN:NADP+ OXIDOREDUCTASE (FERREDOXIN REDUCTASE) MUTANT E312Q COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FERREDOXIN:NADP+ OXIDOREDUCTASE); COMPND 3 CHAIN: A; COMPND 4 EC: 1.18.1.2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 3 ORGANISM_COMMON: SPINACH; SOURCE 4 ORGANISM_TAXID: 3562; SOURCE 5 ORGAN: LEAF; SOURCE 6 ORGANELLE: CHLOROPLAST; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: RRIDM15 KEYWDS FLAVOPROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ALIVERTI,Z.DENG,D.RAVASI,L.PIUBELLI,P.A.KARPLUS,G.ZANETTI REVDAT 6 09-AUG-23 1BX1 1 REMARK SEQADV REVDAT 5 14-MAR-18 1BX1 1 SEQADV REVDAT 4 24-FEB-09 1BX1 1 VERSN REVDAT 3 01-APR-03 1BX1 1 JRNL REVDAT 2 22-DEC-99 1BX1 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 14-OCT-98 1BX1 0 JRNL AUTH A.ALIVERTI,Z.DENG,D.RAVASI,L.PIUBELLI,P.A.KARPLUS,G.ZANETTI JRNL TITL PROBING THE FUNCTION OF THE INVARIANT GLUTAMYL RESIDUE 312 JRNL TITL 2 IN SPINACH FERREDOXIN-NADP+ REDUCTASE. JRNL REF J.BIOL.CHEM. V. 273 34008 1998 JRNL REFN ISSN 0021-9258 JRNL PMID 9852055 JRNL DOI 10.1074/JBC.273.51.34008 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 26954 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3233 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2356 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.280 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAFAD.PRO REMARK 3 PARAMETER FILE 3 : PARAM19.SOL REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPFAD.PRO REMARK 3 TOPOLOGY FILE 3 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008131. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SDMS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27319 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29100 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1FNB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.00000 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 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 GLN A 1 REMARK 465 ILE A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 ASP A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 7 REMARK 465 ALA A 8 REMARK 465 PRO A 9 REMARK 465 PRO A 10 REMARK 465 PRO A 11 REMARK 465 ALA A 12 REMARK 465 PRO A 13 REMARK 465 ALA A 14 REMARK 465 LYS A 15 REMARK 465 VAL A 16 REMARK 465 GLU A 17 REMARK 465 LYS A 18 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 53 128.71 -30.20 REMARK 500 TYR A 212 17.21 59.11 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 PO4 A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 317 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 315 DBREF 1BX1 A 1 314 UNP P00455 FENR_SPIOL 56 369 SEQADV 1BX1 GLN A 312 UNP P00455 GLU 367 ENGINEERED MUTATION SEQRES 1 A 314 GLN ILE ALA SER ASP VAL GLU ALA PRO PRO PRO ALA PRO SEQRES 2 A 314 ALA LYS VAL GLU LYS HIS SER LYS LYS MET GLU GLU GLY SEQRES 3 A 314 ILE THR VAL ASN LYS PHE LYS PRO LYS THR PRO TYR VAL SEQRES 4 A 314 GLY ARG CYS LEU LEU ASN THR LYS ILE THR GLY ASP ASP SEQRES 5 A 314 ALA PRO GLY GLU THR TRP HIS MET VAL PHE SER HIS GLU SEQRES 6 A 314 GLY GLU ILE PRO TYR ARG GLU GLY GLN SER VAL GLY VAL SEQRES 7 A 314 ILE PRO ASP GLY GLU ASP LYS ASN GLY LYS PRO HIS LYS SEQRES 8 A 314 LEU ARG LEU TYR SER ILE ALA SER SER ALA LEU GLY ASP SEQRES 9 A 314 PHE GLY ASP ALA LYS SER VAL SER LEU CYS VAL LYS ARG SEQRES 10 A 314 LEU ILE TYR THR ASN ASP ALA GLY GLU THR ILE LYS GLY SEQRES 11 A 314 VAL CYS SER ASN PHE LEU CYS ASP LEU LYS PRO GLY ALA SEQRES 12 A 314 GLU VAL LYS LEU THR GLY PRO VAL GLY LYS GLU MET LEU SEQRES 13 A 314 MET PRO LYS ASP PRO ASN ALA THR ILE ILE MET LEU GLY SEQRES 14 A 314 THR GLY THR GLY ILE ALA PRO PHE ARG SER PHE LEU TRP SEQRES 15 A 314 LYS MET PHE PHE GLU LYS HIS ASP ASP TYR LYS PHE ASN SEQRES 16 A 314 GLY LEU ALA TRP LEU PHE LEU GLY VAL PRO THR SER SER SEQRES 17 A 314 SER LEU LEU TYR LYS GLU GLU PHE GLU LYS MET LYS GLU SEQRES 18 A 314 LYS ALA PRO ASP ASN PHE ARG LEU ASP PHE ALA VAL SER SEQRES 19 A 314 ARG GLU GLN THR ASN GLU LYS GLY GLU LYS MET TYR ILE SEQRES 20 A 314 GLN THR ARG MET ALA GLN TYR ALA VAL GLU LEU TRP GLU SEQRES 21 A 314 MET LEU LYS LYS ASP ASN THR TYR PHE TYR MET CYS GLY SEQRES 22 A 314 LEU LYS GLY MET GLU LYS GLY ILE ASP ASP ILE MET VAL SEQRES 23 A 314 SER LEU ALA ALA ALA GLU GLY ILE ASP TRP ILE GLU TYR SEQRES 24 A 314 LYS ARG GLN LEU LYS LYS ALA GLU GLN TRP ASN VAL GLN SEQRES 25 A 314 VAL TYR HET PO4 A 316 5 HET SO4 A 317 5 HET FAD A 315 53 HETNAM PO4 PHOSPHATE ION HETNAM SO4 SULFATE ION HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 PO4 O4 P 3- FORMUL 3 SO4 O4 S 2- FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 HOH *221(H2 O) HELIX 1 1 PRO A 34 THR A 36 5 3 HELIX 2 2 VAL A 131 ASP A 138 1 8 HELIX 3 3 GLY A 171 PHE A 185 5 15 HELIX 4 4 SER A 207 SER A 209 5 3 HELIX 5 5 LYS A 213 LYS A 222 1 10 HELIX 6 6 ILE A 247 LYS A 263 1 17 HELIX 7 7 LYS A 275 GLU A 292 5 18 HELIX 8 8 TRP A 296 LYS A 305 1 10 SHEET 1 A 6 ARG A 93 SER A 96 0 SHEET 2 A 6 SER A 75 ILE A 79 -1 N VAL A 78 O ARG A 93 SHEET 3 A 6 GLU A 144 THR A 148 -1 N THR A 148 O GLY A 77 SHEET 4 A 6 TYR A 38 LYS A 47 -1 N GLY A 40 O VAL A 145 SHEET 5 A 6 THR A 57 SER A 63 -1 N SER A 63 O ARG A 41 SHEET 6 A 6 SER A 110 LYS A 116 -1 N VAL A 115 O TRP A 58 SHEET 1 B 2 ILE A 119 THR A 121 0 SHEET 2 B 2 THR A 127 LYS A 129 -1 N ILE A 128 O TYR A 120 SHEET 1 C 5 TRP A 309 TYR A 314 0 SHEET 2 C 5 THR A 267 LEU A 274 1 N PHE A 269 O ASN A 310 SHEET 3 C 5 THR A 164 THR A 170 1 N THR A 164 O TYR A 268 SHEET 4 C 5 LEU A 197 VAL A 204 1 N LEU A 197 O ILE A 165 SHEET 5 C 5 PHE A 227 VAL A 233 1 N ARG A 228 O ALA A 198 CISPEP 1 GLY A 149 PRO A 150 0 1.22 SITE 1 AC1 6 PRO A 205 SER A 234 ARG A 235 LYS A 244 SITE 2 AC1 6 TYR A 246 HOH A 576 SITE 1 AC2 3 HIS A 90 LYS A 91 ARG A 93 SITE 1 AC3 22 ARG A 93 LEU A 94 TYR A 95 SER A 96 SITE 2 AC3 22 CYS A 114 VAL A 115 LYS A 116 TYR A 120 SITE 3 AC3 22 GLY A 130 VAL A 131 CYS A 132 SER A 133 SITE 4 AC3 22 THR A 172 TYR A 314 HOH A 404 HOH A 406 SITE 5 AC3 22 HOH A 407 HOH A 418 HOH A 423 HOH A 526 SITE 6 AC3 22 HOH A 549 HOH A 591 CRYST1 90.800 58.000 68.100 90.00 99.70 90.00 C 1 2 1 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 0.011013 0.000000 0.001882 0.00000 SCALE2 0.000000 0.017241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014897 0.00000