HEADER OXIDOREDUCTASE 06-FEB-12 4DL9 TITLE CRYSTAL STRUCTURE OF S-NITROSOGLUTATHIONE REDUCTASE FROM TOMATO TITLE 2 (SOLANUM LYCOPERSICUM) IN COMPLEX WITH NAD+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALCOHOL DEHYDROGENASE CLASS III; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM LYCOPERSICUM; SOURCE 3 ORGANISM_COMMON: TOMATO; SOURCE 4 ORGANISM_TAXID: 4081; SOURCE 5 STRAIN: CV. AMATEUR; SOURCE 6 GENE: ADH3, GSNOR; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: T7 EXPRESS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCDFDUET KEYWDS ROSSMANN FOLD, OXIDOREDUCTASE, ALCOHOL DEHYDROGENASE CLASS-3, S- KEYWDS 2 NITROSOGLUTATHIONE, NAD+ EXPDTA X-RAY DIFFRACTION AUTHOR D.KOPECNY,M.TYLICHOVA,P.BRIOZZO REVDAT 4 13-SEP-23 4DL9 1 REMARK SEQADV LINK REVDAT 3 20-MAR-13 4DL9 1 JRNL REVDAT 2 23-JAN-13 4DL9 1 JRNL REVDAT 1 26-DEC-12 4DL9 0 JRNL AUTH L.KUBIENOVA,D.KOPECNY,M.TYLICHOVA,P.BRIOZZO,J.SKOPALOVA, JRNL AUTH 2 M.SEBELA,M.NAVRATIL,R.TACHE,L.LUHOVA,J.B.BARROSO, JRNL AUTH 3 M.PETRIVALSKY JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A PLANT JRNL TITL 2 S-NITROSOGLUTATHIONE REDUCTASE FROM SOLANUM LYCOPERSICUM. JRNL REF BIOCHIMIE V. 95 889 2013 JRNL REFN ISSN 0300-9084 JRNL PMID 23274177 JRNL DOI 10.1016/J.BIOCHI.2012.12.009 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 67833 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3437 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 : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.57 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 4838 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2434 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4607 REMARK 3 BIN R VALUE (WORKING SET) : 0.2407 REMARK 3 BIN FREE R VALUE : 0.2975 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.77 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 231 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 : 5698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 622 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.30340 REMARK 3 B22 (A**2) : 9.65520 REMARK 3 B33 (A**2) : 5.64820 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.222 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.131 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5969 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8114 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2055 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 133 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 911 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5969 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 786 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 7619 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.09 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.57 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.70 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4DL9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68193 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.210 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: PDB ENTRY 1TEH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 14% PEG 20000, 4% REMARK 280 GLYCEROL (PLUS 2.5 MM NAD+ IN THE DROP), VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 41.05700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 62.53800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.05700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 62.53800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 B 791 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 MET A -16 REMARK 465 GLY A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 SER A -6 REMARK 465 GLN A -5 REMARK 465 ASP A -4 REMARK 465 PRO A -3 REMARK 465 ASN A -2 REMARK 465 SER A -1 REMARK 465 SER A 0 REMARK 465 MET B -16 REMARK 465 GLY B -15 REMARK 465 SER B -14 REMARK 465 SER B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 SER B -6 REMARK 465 GLN B -5 REMARK 465 ASP B -4 REMARK 465 PRO B -3 REMARK 465 ASN B -2 REMARK 465 SER B -1 REMARK 465 SER B 0 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 69 -1.87 -145.52 REMARK 500 ARG A 100 -7.82 75.13 REMARK 500 MET A 144 16.84 56.56 REMARK 500 THR A 146 -51.44 -121.35 REMARK 500 CYS A 177 -97.24 -147.78 REMARK 500 LEU A 203 45.59 -108.43 REMARK 500 ILE A 272 -45.65 -133.75 REMARK 500 TRP A 289 -8.00 -145.51 REMARK 500 VAL A 345 -50.57 -139.63 REMARK 500 ASP A 369 49.39 -107.83 REMARK 500 LEU A 371 -117.82 -109.63 REMARK 500 ARG B 100 -10.47 70.66 REMARK 500 CYS B 177 -95.55 -152.52 REMARK 500 LEU B 203 52.09 -108.46 REMARK 500 TRP B 289 -9.76 -148.35 REMARK 500 VAL B 345 -48.66 -138.38 REMARK 500 LEU B 371 -119.42 -106.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 47 SG REMARK 620 2 HIS A 69 NE2 97.2 REMARK 620 3 GLU A 70 OE2 107.1 114.4 REMARK 620 4 CYS A 177 SG 128.5 106.4 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 99 SG REMARK 620 2 CYS A 102 SG 108.9 REMARK 620 3 CYS A 105 SG 117.1 104.2 REMARK 620 4 CYS A 113 SG 103.2 120.6 103.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 47 SG REMARK 620 2 HIS B 69 NE2 98.6 REMARK 620 3 GLU B 70 OE2 105.6 117.1 REMARK 620 4 CYS B 177 SG 128.5 104.0 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 99 SG REMARK 620 2 CYS B 102 SG 107.9 REMARK 620 3 CYS B 105 SG 117.0 104.0 REMARK 620 4 CYS B 113 SG 104.3 119.8 104.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DLA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF S-NITROSOGLUTATHIONE REDUCTASE APOENZYME FROM REMARK 900 TOMATO (SOLANUM LYCOPERSICUM) REMARK 900 RELATED ID: 4DLB RELATED DB: PDB REMARK 900 STRUCTURE OF S-NITROSOGLUTATHIONE REDUCTASE FROM TOMATO (SOLANUM REMARK 900 LYCOPERSICUM) CRYSTALLIZED IN PRESENCE OF NADH AND GLUTATHIONE DBREF 4DL9 A 2 379 UNP D2Y3F4 D2Y3F4_SOLLC 2 379 DBREF 4DL9 B 2 379 UNP D2Y3F4 D2Y3F4_SOLLC 2 379 SEQADV 4DL9 MET A -16 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 GLY A -15 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER A -14 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER A -13 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS A -12 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS A -11 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS A -10 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS A -9 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS A -8 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS A -7 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER A -6 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 GLN A -5 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 ASP A -4 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 PRO A -3 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 ASN A -2 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER A -1 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER A 0 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER A 1 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 MET B -16 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 GLY B -15 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER B -14 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER B -13 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS B -12 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS B -11 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS B -10 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS B -9 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS B -8 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 HIS B -7 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER B -6 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 GLN B -5 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 ASP B -4 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 PRO B -3 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 ASN B -2 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER B -1 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER B 0 UNP D2Y3F4 EXPRESSION TAG SEQADV 4DL9 SER B 1 UNP D2Y3F4 EXPRESSION TAG SEQRES 1 A 396 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 396 PRO ASN SER SER SER ALA THR GLN GLY GLN VAL ILE THR SEQRES 3 A 396 CYS LYS ALA ALA VAL ALA TRP GLU PRO ASN LYS PRO LEU SEQRES 4 A 396 VAL ILE GLU ASP VAL GLN VAL ALA PRO PRO GLN ALA GLY SEQRES 5 A 396 GLU VAL ARG VAL LYS VAL LEU TYR THR ALA LEU CYS HIS SEQRES 6 A 396 THR ASP ALA TYR THR TRP SER GLY LYS ASP PRO GLU GLY SEQRES 7 A 396 LEU PHE PRO CYS VAL LEU GLY HIS GLU ALA ALA GLY ILE SEQRES 8 A 396 VAL GLU SER VAL GLY GLU GLY VAL THR GLU VAL GLN PRO SEQRES 9 A 396 GLY ASP HIS VAL ILE PRO CYS TYR GLN ALA GLU CYS ARG SEQRES 10 A 396 GLU CYS LYS PHE CYS LYS SER GLY LYS THR ASN LEU CYS SEQRES 11 A 396 GLY LYS VAL ARG ALA ALA THR GLY VAL GLY VAL MET MET SEQRES 12 A 396 ASN ASP ARG LYS SER ARG PHE SER ILE ASN GLY LYS PRO SEQRES 13 A 396 ILE TYR HIS PHE MET GLY THR SER THR PHE SER GLN TYR SEQRES 14 A 396 THR VAL VAL HIS ASP VAL SER VAL ALA LYS ILE ASP PRO SEQRES 15 A 396 VAL ALA PRO LEU GLU LYS VAL CYS LEU LEU GLY CYS GLY SEQRES 16 A 396 VAL PRO THR GLY LEU GLY ALA VAL TRP ASN THR ALA LYS SEQRES 17 A 396 VAL GLU PRO GLY SER ILE VAL ALA VAL PHE GLY LEU GLY SEQRES 18 A 396 THR VAL GLY LEU ALA VAL ALA GLU GLY ALA LYS ALA ALA SEQRES 19 A 396 GLY ALA SER ARG ILE ILE GLY ILE ASP ILE ASP SER LYS SEQRES 20 A 396 LYS PHE ASP ARG ALA LYS ASN PHE GLY VAL THR GLU PHE SEQRES 21 A 396 ILE ASN PRO LYS GLU HIS GLU GLN PRO ILE GLN GLN VAL SEQRES 22 A 396 ILE VAL ASP LEU THR ASP GLY GLY VAL ASP TYR SER PHE SEQRES 23 A 396 GLU CYS ILE GLY ASN VAL SER VAL MET ARG SER ALA LEU SEQRES 24 A 396 GLU CYS CYS HIS LYS GLY TRP GLY THR SER VAL ILE VAL SEQRES 25 A 396 GLY VAL ALA ALA SER GLY GLN GLU ILE SER THR ARG PRO SEQRES 26 A 396 PHE GLN LEU VAL THR GLY ARG VAL TRP LYS GLY THR ALA SEQRES 27 A 396 PHE GLY GLY PHE LYS SER ARG SER GLN VAL PRO SER LEU SEQRES 28 A 396 VAL ASP LYS TYR LEU LYS LYS GLU ILE LYS VAL ASP GLU SEQRES 29 A 396 TYR ILE THR HIS ASN MET THR LEU ALA ASP ILE ASN LYS SEQRES 30 A 396 ALA PHE ASP LEU MET HIS ASP GLY ASP CYS LEU ARG VAL SEQRES 31 A 396 VAL LEU ASP MET PHE VAL SEQRES 1 B 396 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 B 396 PRO ASN SER SER SER ALA THR GLN GLY GLN VAL ILE THR SEQRES 3 B 396 CYS LYS ALA ALA VAL ALA TRP GLU PRO ASN LYS PRO LEU SEQRES 4 B 396 VAL ILE GLU ASP VAL GLN VAL ALA PRO PRO GLN ALA GLY SEQRES 5 B 396 GLU VAL ARG VAL LYS VAL LEU TYR THR ALA LEU CYS HIS SEQRES 6 B 396 THR ASP ALA TYR THR TRP SER GLY LYS ASP PRO GLU GLY SEQRES 7 B 396 LEU PHE PRO CYS VAL LEU GLY HIS GLU ALA ALA GLY ILE SEQRES 8 B 396 VAL GLU SER VAL GLY GLU GLY VAL THR GLU VAL GLN PRO SEQRES 9 B 396 GLY ASP HIS VAL ILE PRO CYS TYR GLN ALA GLU CYS ARG SEQRES 10 B 396 GLU CYS LYS PHE CYS LYS SER GLY LYS THR ASN LEU CYS SEQRES 11 B 396 GLY LYS VAL ARG ALA ALA THR GLY VAL GLY VAL MET MET SEQRES 12 B 396 ASN ASP ARG LYS SER ARG PHE SER ILE ASN GLY LYS PRO SEQRES 13 B 396 ILE TYR HIS PHE MET GLY THR SER THR PHE SER GLN TYR SEQRES 14 B 396 THR VAL VAL HIS ASP VAL SER VAL ALA LYS ILE ASP PRO SEQRES 15 B 396 VAL ALA PRO LEU GLU LYS VAL CYS LEU LEU GLY CYS GLY SEQRES 16 B 396 VAL PRO THR GLY LEU GLY ALA VAL TRP ASN THR ALA LYS SEQRES 17 B 396 VAL GLU PRO GLY SER ILE VAL ALA VAL PHE GLY LEU GLY SEQRES 18 B 396 THR VAL GLY LEU ALA VAL ALA GLU GLY ALA LYS ALA ALA SEQRES 19 B 396 GLY ALA SER ARG ILE ILE GLY ILE ASP ILE ASP SER LYS SEQRES 20 B 396 LYS PHE ASP ARG ALA LYS ASN PHE GLY VAL THR GLU PHE SEQRES 21 B 396 ILE ASN PRO LYS GLU HIS GLU GLN PRO ILE GLN GLN VAL SEQRES 22 B 396 ILE VAL ASP LEU THR ASP GLY GLY VAL ASP TYR SER PHE SEQRES 23 B 396 GLU CYS ILE GLY ASN VAL SER VAL MET ARG SER ALA LEU SEQRES 24 B 396 GLU CYS CYS HIS LYS GLY TRP GLY THR SER VAL ILE VAL SEQRES 25 B 396 GLY VAL ALA ALA SER GLY GLN GLU ILE SER THR ARG PRO SEQRES 26 B 396 PHE GLN LEU VAL THR GLY ARG VAL TRP LYS GLY THR ALA SEQRES 27 B 396 PHE GLY GLY PHE LYS SER ARG SER GLN VAL PRO SER LEU SEQRES 28 B 396 VAL ASP LYS TYR LEU LYS LYS GLU ILE LYS VAL ASP GLU SEQRES 29 B 396 TYR ILE THR HIS ASN MET THR LEU ALA ASP ILE ASN LYS SEQRES 30 B 396 ALA PHE ASP LEU MET HIS ASP GLY ASP CYS LEU ARG VAL SEQRES 31 B 396 VAL LEU ASP MET PHE VAL HET ZN A 401 1 HET ZN A 402 1 HET NAD A 403 44 HET GOL A 404 6 HET MES A 405 12 HET ZN B 401 1 HET ZN B 402 1 HET NAD B 403 44 HET GOL B 404 6 HET MES B 405 12 HETNAM ZN ZINC ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 4(ZN 2+) FORMUL 5 NAD 2(C21 H27 N7 O14 P2) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 7 MES 2(C6 H13 N O4 S) FORMUL 13 HOH *622(H2 O) HELIX 1 1 CYS A 47 GLY A 56 1 10 HELIX 2 2 VAL A 116 GLY A 121 1 6 HELIX 3 3 PRO A 168 CYS A 173 1 6 HELIX 4 4 LEU A 174 GLY A 176 5 3 HELIX 5 5 CYS A 177 ASN A 188 1 12 HELIX 6 6 GLY A 204 ALA A 217 1 14 HELIX 7 7 ASP A 228 LYS A 230 5 3 HELIX 8 8 LYS A 231 LYS A 236 1 6 HELIX 9 9 ASN A 237 GLY A 239 5 3 HELIX 10 10 ASN A 245 HIS A 249 5 5 HELIX 11 11 PRO A 252 THR A 261 1 10 HELIX 12 12 ASN A 274 CYS A 284 1 11 HELIX 13 13 PRO A 308 THR A 313 1 6 HELIX 14 14 ALA A 321 PHE A 325 5 5 HELIX 15 15 LYS A 326 LYS A 340 1 15 HELIX 16 16 VAL A 345 GLU A 347 5 3 HELIX 17 17 ASP A 357 GLY A 368 1 12 HELIX 18 18 CYS B 47 SER B 55 1 9 HELIX 19 19 CYS B 102 GLY B 108 1 7 HELIX 20 20 VAL B 116 GLY B 121 1 6 HELIX 21 21 PRO B 168 CYS B 173 1 6 HELIX 22 22 LEU B 174 GLY B 176 5 3 HELIX 23 23 CYS B 177 ASN B 188 1 12 HELIX 24 24 GLY B 204 ALA B 217 1 14 HELIX 25 25 ASP B 228 LYS B 230 5 3 HELIX 26 26 LYS B 231 ASN B 237 1 7 HELIX 27 27 ASN B 245 HIS B 249 5 5 HELIX 28 28 PRO B 252 THR B 261 1 10 HELIX 29 29 ASN B 274 CYS B 284 1 11 HELIX 30 30 PRO B 308 THR B 313 1 6 HELIX 31 31 ALA B 321 PHE B 325 5 5 HELIX 32 32 LYS B 326 LYS B 340 1 15 HELIX 33 33 VAL B 345 GLU B 347 5 3 HELIX 34 34 ASP B 357 GLY B 368 1 12 SHEET 1 A 4 ILE A 8 VAL A 14 0 SHEET 2 A 4 VAL A 23 VAL A 29 -1 O GLU A 25 N ALA A 12 SHEET 3 A 4 PHE A 133 ILE A 135 -1 O SER A 134 N GLN A 28 SHEET 4 A 4 LYS A 138 ILE A 140 -1 O ILE A 140 N PHE A 133 SHEET 1 B 5 TYR A 152 HIS A 156 0 SHEET 2 B 5 GLU A 36 ALA A 45 -1 N VAL A 39 O THR A 153 SHEET 3 B 5 GLU A 70 VAL A 78 -1 O ILE A 74 N LYS A 40 SHEET 4 B 5 HIS A 90 PRO A 93 -1 O VAL A 91 N GLY A 73 SHEET 5 B 5 VAL A 160 ILE A 163 -1 O ILE A 163 N HIS A 90 SHEET 1 C 4 TYR A 152 HIS A 156 0 SHEET 2 C 4 GLU A 36 ALA A 45 -1 N VAL A 39 O THR A 153 SHEET 3 C 4 ARG A 372 ASP A 376 -1 O LEU A 375 N THR A 44 SHEET 4 C 4 ILE A 349 THR A 354 1 N MET A 353 O VAL A 374 SHEET 1 D 6 GLU A 242 ILE A 244 0 SHEET 2 D 6 ARG A 221 ILE A 225 1 N GLY A 224 O GLU A 242 SHEET 3 D 6 ILE A 197 PHE A 201 1 N VAL A 198 O ILE A 223 SHEET 4 D 6 TYR A 267 GLU A 270 1 O PHE A 269 N PHE A 201 SHEET 5 D 6 THR A 291 ILE A 294 1 O VAL A 293 N SER A 268 SHEET 6 D 6 VAL A 316 GLY A 319 1 O LYS A 318 N ILE A 294 SHEET 1 E 2 ILE A 304 THR A 306 0 SHEET 2 E 2 ILE B 304 THR B 306 -1 O THR B 306 N ILE A 304 SHEET 1 F 4 ILE B 8 VAL B 14 0 SHEET 2 F 4 VAL B 23 VAL B 29 -1 O VAL B 29 N ILE B 8 SHEET 3 F 4 PHE B 133 ILE B 135 -1 O SER B 134 N GLN B 28 SHEET 4 F 4 LYS B 138 ILE B 140 -1 O LYS B 138 N ILE B 135 SHEET 1 G 5 TYR B 152 HIS B 156 0 SHEET 2 G 5 GLU B 36 ALA B 45 -1 N VAL B 39 O THR B 153 SHEET 3 G 5 GLU B 70 VAL B 78 -1 O ILE B 74 N LYS B 40 SHEET 4 G 5 HIS B 90 PRO B 93 -1 O VAL B 91 N GLY B 73 SHEET 5 G 5 VAL B 160 ILE B 163 -1 O ILE B 163 N HIS B 90 SHEET 1 H 4 TYR B 152 HIS B 156 0 SHEET 2 H 4 GLU B 36 ALA B 45 -1 N VAL B 39 O THR B 153 SHEET 3 H 4 ARG B 372 ASP B 376 -1 O LEU B 375 N THR B 44 SHEET 4 H 4 ILE B 349 THR B 354 1 N MET B 353 O VAL B 374 SHEET 1 I 6 GLU B 242 ILE B 244 0 SHEET 2 I 6 ARG B 221 ILE B 225 1 N GLY B 224 O GLU B 242 SHEET 3 I 6 ILE B 197 PHE B 201 1 N VAL B 198 O ILE B 223 SHEET 4 I 6 TYR B 267 GLU B 270 1 O PHE B 269 N PHE B 201 SHEET 5 I 6 THR B 291 ILE B 294 1 O VAL B 293 N SER B 268 SHEET 6 I 6 VAL B 316 GLY B 319 1 O VAL B 316 N SER B 292 LINK SG CYS A 47 ZN ZN A 401 1555 1555 2.24 LINK NE2 HIS A 69 ZN ZN A 401 1555 1555 2.05 LINK OE2 GLU A 70 ZN ZN A 401 1555 1555 2.03 LINK SG CYS A 99 ZN ZN A 402 1555 1555 2.40 LINK SG CYS A 102 ZN ZN A 402 1555 1555 2.26 LINK SG CYS A 105 ZN ZN A 402 1555 1555 2.34 LINK SG CYS A 113 ZN ZN A 402 1555 1555 2.21 LINK SG CYS A 177 ZN ZN A 401 1555 1555 2.34 LINK SG CYS B 47 ZN ZN B 401 1555 1555 2.18 LINK NE2 HIS B 69 ZN ZN B 401 1555 1555 2.21 LINK OE2 GLU B 70 ZN ZN B 401 1555 1555 2.03 LINK SG CYS B 99 ZN ZN B 402 1555 1555 2.40 LINK SG CYS B 102 ZN ZN B 402 1555 1555 2.24 LINK SG CYS B 105 ZN ZN B 402 1555 1555 2.31 LINK SG CYS B 113 ZN ZN B 402 1555 1555 2.19 LINK SG CYS B 177 ZN ZN B 401 1555 1555 2.33 CISPEP 1 PHE A 63 PRO A 64 0 0.06 CISPEP 2 PHE B 63 PRO B 64 0 -4.63 SITE 1 AC1 5 CYS A 47 HIS A 69 GLU A 70 CYS A 177 SITE 2 AC1 5 ARG A 372 SITE 1 AC2 4 CYS A 99 CYS A 102 CYS A 105 CYS A 113 SITE 1 AC3 34 TYR A 95 CYS A 177 THR A 181 GLY A 202 SITE 2 AC3 34 GLY A 204 THR A 205 VAL A 206 ASP A 226 SITE 3 AC3 34 ILE A 227 LYS A 231 CYS A 271 ILE A 272 SITE 4 AC3 34 GLY A 273 VAL A 277 VAL A 295 GLY A 296 SITE 5 AC3 34 VAL A 297 THR A 320 ALA A 321 PHE A 322 SITE 6 AC3 34 ARG A 372 HOH A 501 HOH A 504 HOH A 505 SITE 7 AC3 34 HOH A 506 HOH A 510 HOH A 511 HOH A 512 SITE 8 AC3 34 HOH A 562 HOH A 666 HOH A 685 HOH A 692 SITE 9 AC3 34 HOH A 778 HOH A 793 SITE 1 AC4 7 TRP A 187 ALA A 216 ALA A 217 LYS A 337 SITE 2 AC4 7 HOH A 582 HOH A 708 HOH A 736 SITE 1 AC5 6 ARG A 307 PHE A 309 HOH A 646 GLU B 60 SITE 2 AC5 6 SER B 300 GLY B 301 SITE 1 AC6 5 CYS B 47 HIS B 69 GLU B 70 CYS B 177 SITE 2 AC6 5 ARG B 372 SITE 1 AC7 4 CYS B 99 CYS B 102 CYS B 105 CYS B 113 SITE 1 AC8 32 TYR B 95 CYS B 177 THR B 181 GLY B 202 SITE 2 AC8 32 GLY B 204 THR B 205 VAL B 206 ASP B 226 SITE 3 AC8 32 ILE B 227 LYS B 231 CYS B 271 ILE B 272 SITE 4 AC8 32 VAL B 277 VAL B 295 GLY B 296 VAL B 297 SITE 5 AC8 32 THR B 320 ALA B 321 PHE B 322 ARG B 372 SITE 6 AC8 32 HOH B 504 HOH B 505 HOH B 508 HOH B 509 SITE 7 AC8 32 HOH B 638 HOH B 653 HOH B 689 HOH B 712 SITE 8 AC8 32 HOH B 713 HOH B 725 HOH B 756 HOH B 809 SITE 1 AC9 4 TRP B 187 ALA B 217 LYS B 337 HOH B 555 SITE 1 BC1 6 GLU A 60 SER A 300 GLY A 301 ARG B 307 SITE 2 BC1 6 PHE B 309 HOH B 686 CRYST1 82.114 125.076 76.761 90.00 90.00 90.00 P 21 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 0.012178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007995 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013027 0.00000