HEADER SULFURTRANSFERASE 24-JUL-95 1ORA OBSLTE 01-AUG-96 1ORA 2ORA TITLE ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY MODIFIED TITLE 2 FORMS OF RHODANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OXIDIZED RHODANESE; COMPND 3 CHAIN: NULL; COMPND 4 EC: 2.8.1.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE KEYWDS THIOSULFATE:CYANIDE SULFURTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.GLIUBICH,M.GAZERRO,G.ZANOTTI,S.DELBONO,R.BERNI REVDAT 1 15-OCT-95 1ORA 0 JRNL AUTH F.GLIUBICH,M.GAZERRO,G.ZANOTTI,S.DELBONO,R.BERNI JRNL TITL ACTIVE SITE STRUCTURAL FEATURES FOR CHEMICALLY JRNL TITL 2 MODIFIED FORMS OF RHODANESE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.G.J.HOL,L.J.LIJK,K.H.KALK REMARK 1 TITL THE HIGH RESOLUTION THREE-DIMENSIONAL STRUCTURE OF REMARK 1 TITL 2 BOVINE LIVER RHODANESE REMARK 1 REF FUNDAM.APPL.TOXICOL. V. 3 370 1983 REMARK 1 REFN ASTM FAATDF US ISSN 0272-0590 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.H.PLOEGMAN,G.DRENT,K.H.KALK,W.G.J.HOL REMARK 1 TITL THE STRUCTURE OF BOVINE LIVER RHODANESE: THE REMARK 1 TITL 2 ACTIVE SITE IN THE SULFUR-SUBSTITUTED AND THE REMARK 1 TITL 3 SULFUR-FREE ENZYME REMARK 1 REF J.MOL.BIOL. V. 127 149 1979 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.H.PLOEGMAN,G.DRENT,K.H.KALK,W.G.J.HOL, REMARK 1 AUTH 2 W.G.J.HEINRIKSON,R.L.KEIM,P.S.WENG,J.RUSSEL REMARK 1 TITL THE COVALENT AND TERTIARY STRUCTURE OF BOVINE REMARK 1 TITL 2 LIVER RHODANESE REMARK 1 REF NATURE V. 273 124 1978 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 1ORA REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12406 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :NULL REMARK 3 FREE R VALUE TEST SET SELECTION :NULL REMARK 3 R VALUE (WORKING + TEST SET) :0.179 REMARK 3 R VALUE (WORKING SET) :NULL 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 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : NULL ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ORA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 1ORA THE ENZYME WAS OXIDIZED WITH HYDROGEN PEROXIDE AT CYS REMARK 5 247. 1ORA THE OXIDATION WITH H2O2 PRODUCED A BOND BETWEEN REMARK 5 SG OF CYS 1ORA 247 AND OG OF SER 181. 1ORA REMARK 18 REMARK 18 1ORA EXPERIMENTAL DETAILS. 1ORA DATE OF DATA COLLECTION : REMARK 18 DEC-94 1ORA MONOCHROMATIC (Y/N) : Y 1ORA LAUE (Y/N) : N REMARK 18 1ORA WAVELENGTH OR RANGE (A) : 1.5418 1ORA DETECTOR TYPE : REMARK 18 XENTRONIX X1000 1ORA DETECTOR MANUFACTURER : SIEMENS 1ORA REMARK 18 INTENSITY-INTEGRATION SOFTWARE : SAINT 1ORA DATA REDUNDANCY REMARK 18 : 3 1ORA MERGING R VALUE (INTENSITY) : 0.086 1ORA REMARK 19 REMARK 19 1ORA SOLVENT CONTENT (VS) : 49. % 1ORA REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-1994 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : N 1ORA REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : XENTRONIX X1000 1ORA REMARK 200 DETECTOR MANUFACTURER : SIEMENS 1ORA REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT 1ORA REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 78.11500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.52000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.11500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.52000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 GLY 294 REMARK 465 LYS 295 REMARK 465 ALA 296 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 REMARK 500 OG SER 181 SG CYS 247 1.79 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA 183 N ALA 183 CA 0.140 REMARK 500 ALA 183 CA ALA 183 C 0.142 REMARK 500 ARG 182 C ALA 183 N -0.144 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 364 DISTANCE = 5.04 ANGSTROMS REMARK 525 HOH 372 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH 386 DISTANCE = 7.15 ANGSTROMS REMARK 999 REMARK 999 1ORA CROSS REFERENCE TO SEQUENCE DATABASE 1ORA SWISS-PROT REMARK 999 ENTRY NAME PDB ENTRY CHAIN NAME 1ORA THTR_BOVIN 1ORA 1ORA REMARK 999 SEQUENCE 1ORA MODRES: 1ORA CYS() 247() OXIDATION WITH REMARK 999 HYDROGEN 1ORA PEROXIDE PRODUCED A BOND OF SG 247 WITH OG OF REMARK 999 SER 181 1ORA MODRES: 1ORA SER() 181() SEE PREVIOUS COMMENT REMARK 999 1ORA SEQRES 1 296 VAL HIS GLN VAL LEU TYR ARG ALA LEU VAL SER THR LYS SEQRES 2 296 TRP LEU ALA GLU SER VAL ARG ALA GLY LYS VAL GLY PRO SEQRES 3 296 GLY LEU ARG VAL LEU ASP ALA SER TRP TYR SER PRO GLY SEQRES 4 296 THR ARG GLU ALA ARG LYS GLU TYR LEU GLU ARG HIS VAL SEQRES 5 296 PRO GLY ALA SER PHE PHE ASP ILE GLU GLU CYS ARG ASP SEQRES 6 296 LYS ALA SER PRO TYR GLU VAL MET LEU PRO SER GLU ALA SEQRES 7 296 GLY PHE ALA ASP TYR VAL GLY SER LEU GLY ILE SER ASN SEQRES 8 296 ASP THR HIS VAL VAL VAL TYR ASP GLY ASP ASP LEU GLY SEQRES 9 296 SER PHE TYR ALA PRO ARG VAL TRP TRP MET PHE ARG VAL SEQRES 10 296 PHE GLY HIS ARG THR VAL SER VAL LEU ASN GLY GLY PHE SEQRES 11 296 ARG ASN TRP LEU LYS GLU GLY HIS PRO VAL THR SER GLU SEQRES 12 296 PRO SER ARG PRO GLU PRO ALA ILE PHE LYS ALA THR LEU SEQRES 13 296 ASN ARG SER LEU LEU LYS THR TYR GLU GLN VAL LEU GLU SEQRES 14 296 ASN LEU GLU SER LYS ARG PHE GLN LEU VAL ASP SER ARG SEQRES 15 296 ALA GLN GLY ARG TYR LEU GLY THR GLN PRO GLU PRO ASP SEQRES 16 296 ALA VAL GLY LEU ASP SER GLY HIS ILE ARG GLY SER VAL SEQRES 17 296 ASN MET PRO PHE MET ASN PHE LEU THR GLU ASP GLY PHE SEQRES 18 296 GLU LYS SER PRO GLU GLU LEU ARG ALA MET PHE GLU ALA SEQRES 19 296 LYS LYS VAL ASP LEU THR LYS PRO LEU ILE ALA THR CYS SEQRES 20 296 ARG LYS GLY VAL THR ALA CYS HIS ILE ALA LEU ALA ALA SEQRES 21 296 TYR LEU CYS GLY LYS PRO ASP VAL ALA ILE TYR ASP GLY SEQRES 22 296 SER TRP PHE GLU TRP PHE HIS ARG ALA PRO PRO GLU THR SEQRES 23 296 TRP VAL SER GLN GLY LYS GLY GLY LYS ALA FORMUL 2 HOH *87(H2 O1) HELIX 1 1 THR 12 ARG 20 1 9 HELIX 2 2 ALA 43 GLU 49 1 7 HELIX 3 3 GLU 77 LEU 87 1 11 HELIX 4 4 ALA 108 VAL 117 1 10 HELIX 5 5 GLY 129 LYS 135 1 7 HELIX 6 6 ARG 158 LEU 160 5 3 HELIX 7 7 TYR 164 SER 173 1 10 HELIX 8 8 GLN 184 LEU 188 1 5 HELIX 9 9 PHE 212 PHE 215 5 4 HELIX 10 10 PRO 225 ALA 234 1 10 HELIX 11 11 ALA 253 LEU 262 1 10 HELIX 12 12 SER 274 ARG 281 1 8 HELIX 13 13 PRO 284 THR 286 5 3 SHEET 1 A 3 LEU 28 ASP 32 0 SHEET 2 A 3 HIS 94 TYR 98 1 N HIS 94 O ARG 29 SHEET 3 A 3 VAL 123 VAL 125 1 N SER 124 O VAL 95 SHEET 1 B 2 GLN 177 ASP 180 0 SHEET 2 B 2 LEU 243 THR 246 1 N ILE 244 O GLN 177 CRYST1 156.230 49.040 42.250 90.00 98.60 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 0.006401 0.000000 0.000968 0.00000 SCALE2 0.000000 0.020392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023938 0.00000