PDB Short entry for 1DWP HEADER HYDROXYNITRILE LYASE 10-DEC-99 1DWP TITLE CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA AT TITLE 2 2.2 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYNITRILE LYASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: (S)-ACETONE-CYANOHYDRIN LYASE, (S)-HYDROXYNITRILASE; COMPND 5 EC: 4.2.1.37; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: ACETATE COMPLEX SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MANIHOT ESCULENTA; SOURCE 3 ORGANISM_COMMON: CASSAVA; SOURCE 4 ORGANISM_TAXID: 3983; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 OTHER_DETAILS: RECOMBINANT PROTEIN KEYWDS HYDROXYNITRILE LYASE, CYANOGENESIS EXPDTA X-RAY DIFFRACTION AUTHOR H.LAUBLE,U.WAGNER,C.KRATKY,B.MIELICH,H.WAJANT,S.FORSTER,F.EFFENBERGER REVDAT 5 08-MAY-24 1DWP 1 REMARK REVDAT 4 24-JUL-19 1DWP 1 REMARK REVDAT 3 24-FEB-09 1DWP 1 VERSN REVDAT 2 26-APR-01 1DWP 1 JRNL REVDAT 1 07-DEC-00 1DWP 0 JRNL AUTH H.LAUBLE,S.FORSTER,B.MIEHLICH,H.WAJANT,F.EFFENBERGER JRNL TITL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN JRNL TITL 2 COMPLEX WITH SUBSTRATES ACETONE AND CHLOROACETONE: JRNL TITL 3 IMPLICATIONS FOR THE MECHANISM OF CYANOGENESIS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 194 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11173464 JRNL DOI 10.1107/S0907444900015766 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 53380 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) : 0.198 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5300 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL 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 : 4178 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 312 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.00 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DWP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1290004336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.905 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NACITRAT, PH 5.4, 6% PEG 8000, REMARK 280 28% MPD, PH 5.40 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 94.50000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.30000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.25000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.30000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 141.75000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.30000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.25000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.30000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.30000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 141.75000 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 94.50000 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 300 REMARK: BIOLOGICAL_UNIT: TETRAMER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.8 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 189.00000 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 PRO B -4 REMARK 465 ILE B -3 REMARK 465 SER B -2 REMARK 465 LYS B -1 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 5 NE2 HIS A 5 CD2 -0.079 REMARK 500 HIS A 10 NE2 HIS A 10 CD2 -0.077 REMARK 500 HIS A 14 NE2 HIS A 14 CD2 -0.072 REMARK 500 HIS A 20 NE2 HIS A 20 CD2 -0.070 REMARK 500 HIS A 31 NE2 HIS A 31 CD2 -0.076 REMARK 500 HIS A 112 NE2 HIS A 112 CD2 -0.078 REMARK 500 HIS B 5 NE2 HIS B 5 CD2 -0.074 REMARK 500 HIS B 10 NE2 HIS B 10 CD2 -0.077 REMARK 500 HIS B 103 NE2 HIS B 103 CD2 -0.067 REMARK 500 HIS B 248 NE2 HIS B 248 CD2 -0.069 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TRP A 17 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP A 17 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 TRP A 19 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 19 CB - CG - CD1 ANGL. DEV. = -8.8 DEGREES REMARK 500 TRP A 19 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP A 19 CG - CD2 - CE3 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 TRP A 128 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 MET A 147 CG - SD - CE ANGL. DEV. = -13.9 DEGREES REMARK 500 VAL A 152 CG1 - CB - CG2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 175 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ILE A 198 CA - CB - CG1 ANGL. DEV. = -13.5 DEGREES REMARK 500 ILE A 198 CA - CB - CG2 ANGL. DEV. = 14.1 DEGREES REMARK 500 TRP A 204 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP A 204 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 206 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP A 218 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TRP A 218 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 HIS B 14 CE1 - NE2 - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 TRP B 17 CD1 - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 TRP B 19 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP B 19 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR B 57 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 GLN B 70 CA - CB - CG ANGL. DEV. = 13.5 DEGREES REMARK 500 ARG B 92 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 92 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 TRP B 128 CD1 - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 TRP B 128 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 155 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 155 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG B 187 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ILE B 198 CA - CB - CG1 ANGL. DEV. = -13.4 DEGREES REMARK 500 ILE B 198 CA - CB - CG2 ANGL. DEV. = 13.5 DEGREES REMARK 500 TRP B 204 CD1 - CG - CD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 TRP B 204 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP B 204 CG - CD2 - CE3 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG B 217 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 TRP B 218 CD1 - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP B 218 CE2 - CD2 - CG ANGL. DEV. = -5.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 13 -24.75 77.94 REMARK 500 SER A 80 -108.44 49.32 REMARK 500 ARG A 129 -116.23 54.37 REMARK 500 THR A 163 152.76 -49.70 REMARK 500 ILE A 210 -40.25 -132.23 REMARK 500 CYS B 13 -20.08 77.32 REMARK 500 HIS B 14 -156.87 -96.51 REMARK 500 SER B 80 -105.14 50.78 REMARK 500 ARG B 129 -116.04 52.92 REMARK 500 PHE B 159 32.13 -99.58 REMARK 500 ILE B 210 -37.55 -138.62 REMARK 500 TYR B 223 81.91 -150.02 REMARK 500 LYS B 237 58.66 -93.77 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 ACT A1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1259 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DWO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN REMARK 900 COMPLEX WITH SUBSTRATES ACETONE AND CHLOROACETONE:IMPLICATIONS FOR REMARK 900 THE MECHANISM OF CYANOGENESIS REMARK 900 RELATED ID: 1DWQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN REMARK 900 COMPLEX WITH SUBSTRATES ACETONE AND CHLOROACETONE:IMPLICATIONS FOR REMARK 900 THE MECHANISM OF CYANOGENESIS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SWISSPROT ENTRY P52705 REPORTS THIS ENZYME TO BE EC 4.2.1.39, REMARK 999 AND TO HAVE A HOMOTRIMERIC SUBUNIT STRUCTURE. THE CORRECT REMARK 999 EC NUMBER IS 4.2.1.37 AND THE MOLECULE IS A TETRAMER. DBREF 1DWP A -4 1 PDB 1DWP 1DWP -4 1 DBREF 1DWP A 2 258 UNP P52705 HNL_MANES 1 257 DBREF 1DWP B -4 1 PDB 1DWP 1DWP -4 1 DBREF 1DWP B 2 258 UNP P52705 HNL_MANES 1 257 SEQADV 1DWP PRO A -4 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP ILE A -3 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP SER A -2 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP LYS A -1 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP MET A 1 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP PRO B -4 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP ILE B -3 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP SER B -2 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP LYS B -1 PDB 1DWP CLONING ARTIFACT SEQADV 1DWP MET B 1 PDB 1DWP CLONING ARTIFACT SEQRES 1 A 262 PRO ILE SER LYS MET VAL THR ALA HIS PHE VAL LEU ILE SEQRES 2 A 262 HIS THR ILE CYS HIS GLY ALA TRP ILE TRP HIS LYS LEU SEQRES 3 A 262 LYS PRO ALA LEU GLU ARG ALA GLY HIS LYS VAL THR ALA SEQRES 4 A 262 LEU ASP MET ALA ALA SER GLY ILE ASP PRO ARG GLN ILE SEQRES 5 A 262 GLU GLN ILE ASN SER PHE ASP GLU TYR SER GLU PRO LEU SEQRES 6 A 262 LEU THR PHE LEU GLU LYS LEU PRO GLN GLY GLU LYS VAL SEQRES 7 A 262 ILE ILE VAL GLY GLU SER CYS ALA GLY LEU ASN ILE ALA SEQRES 8 A 262 ILE ALA ALA ASP ARG TYR VAL ASP LYS ILE ALA ALA GLY SEQRES 9 A 262 VAL PHE HIS ASN SER LEU LEU PRO ASP THR VAL HIS SER SEQRES 10 A 262 PRO SER TYR THR VAL GLU LYS LEU LEU GLU SER PHE PRO SEQRES 11 A 262 ASP TRP ARG ASP THR GLU TYR PHE THR PHE THR ASN ILE SEQRES 12 A 262 THR GLY GLU THR ILE THR THR MET LYS LEU GLY PHE VAL SEQRES 13 A 262 LEU LEU ARG GLU ASN LEU PHE THR LYS CYS THR ASP GLY SEQRES 14 A 262 GLU TYR GLU LEU ALA LYS MET VAL MET ARG LYS GLY SER SEQRES 15 A 262 LEU PHE GLN ASN VAL LEU ALA GLN ARG PRO LYS PHE THR SEQRES 16 A 262 GLU LYS GLY TYR GLY SER ILE LYS LYS VAL TYR ILE TRP SEQRES 17 A 262 THR ASP GLN ASP LYS ILE PHE LEU PRO ASP PHE GLN ARG SEQRES 18 A 262 TRP GLN ILE ALA ASN TYR LYS PRO ASP LYS VAL TYR GLN SEQRES 19 A 262 VAL GLN GLY GLY ASP HIS LYS LEU GLN LEU THR LYS THR SEQRES 20 A 262 GLU GLU VAL ALA HIS ILE LEU GLN GLU VAL ALA ASP ALA SEQRES 21 A 262 TYR ALA SEQRES 1 B 262 PRO ILE SER LYS MET VAL THR ALA HIS PHE VAL LEU ILE SEQRES 2 B 262 HIS THR ILE CYS HIS GLY ALA TRP ILE TRP HIS LYS LEU SEQRES 3 B 262 LYS PRO ALA LEU GLU ARG ALA GLY HIS LYS VAL THR ALA SEQRES 4 B 262 LEU ASP MET ALA ALA SER GLY ILE ASP PRO ARG GLN ILE SEQRES 5 B 262 GLU GLN ILE ASN SER PHE ASP GLU TYR SER GLU PRO LEU SEQRES 6 B 262 LEU THR PHE LEU GLU LYS LEU PRO GLN GLY GLU LYS VAL SEQRES 7 B 262 ILE ILE VAL GLY GLU SER CYS ALA GLY LEU ASN ILE ALA SEQRES 8 B 262 ILE ALA ALA ASP ARG TYR VAL ASP LYS ILE ALA ALA GLY SEQRES 9 B 262 VAL PHE HIS ASN SER LEU LEU PRO ASP THR VAL HIS SER SEQRES 10 B 262 PRO SER TYR THR VAL GLU LYS LEU LEU GLU SER PHE PRO SEQRES 11 B 262 ASP TRP ARG ASP THR GLU TYR PHE THR PHE THR ASN ILE SEQRES 12 B 262 THR GLY GLU THR ILE THR THR MET LYS LEU GLY PHE VAL SEQRES 13 B 262 LEU LEU ARG GLU ASN LEU PHE THR LYS CYS THR ASP GLY SEQRES 14 B 262 GLU TYR GLU LEU ALA LYS MET VAL MET ARG LYS GLY SER SEQRES 15 B 262 LEU PHE GLN ASN VAL LEU ALA GLN ARG PRO LYS PHE THR SEQRES 16 B 262 GLU LYS GLY TYR GLY SER ILE LYS LYS VAL TYR ILE TRP SEQRES 17 B 262 THR ASP GLN ASP LYS ILE PHE LEU PRO ASP PHE GLN ARG SEQRES 18 B 262 TRP GLN ILE ALA ASN TYR LYS PRO ASP LYS VAL TYR GLN SEQRES 19 B 262 VAL GLN GLY GLY ASP HIS LYS LEU GLN LEU THR LYS THR SEQRES 20 B 262 GLU GLU VAL ALA HIS ILE LEU GLN GLU VAL ALA ASP ALA SEQRES 21 B 262 TYR ALA HET ACT A1259 4 HET ACT B1259 4 HETNAM ACT ACETATE ION FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 HOH *312(H2 O) HELIX 1 1 GLY A 15 HIS A 20 5 6 HELIX 2 2 LYS A 21 ALA A 29 1 9 HELIX 3 3 GLN A 47 ILE A 51 5 5 HELIX 4 4 SER A 53 SER A 58 1 6 HELIX 5 5 SER A 58 LEU A 68 1 11 HELIX 6 6 ALA A 82 VAL A 94 1 13 HELIX 7 7 SER A 115 PHE A 125 1 11 HELIX 8 8 GLY A 150 ASN A 157 1 8 HELIX 9 9 THR A 163 MET A 174 1 12 HELIX 10 10 PHE A 180 ARG A 187 1 8 HELIX 11 11 GLY A 194 ILE A 198 5 5 HELIX 12 12 LEU A 212 TYR A 223 1 12 HELIX 13 13 LYS A 237 LYS A 242 1 6 HELIX 14 14 LYS A 242 ALA A 258 1 17 HELIX 15 15 GLY B 15 HIS B 20 5 6 HELIX 16 16 LYS B 21 ALA B 29 1 9 HELIX 17 17 GLN B 47 ILE B 51 5 5 HELIX 18 18 SER B 53 SER B 58 1 6 HELIX 19 19 SER B 58 LEU B 68 1 11 HELIX 20 20 ALA B 82 VAL B 94 1 13 HELIX 21 21 SER B 115 PHE B 125 1 11 HELIX 22 22 GLY B 150 ASN B 157 1 8 HELIX 23 23 THR B 163 MET B 174 1 12 HELIX 24 24 PHE B 180 ARG B 187 1 8 HELIX 25 25 GLY B 194 ILE B 198 5 5 HELIX 26 26 LEU B 212 TYR B 223 1 12 HELIX 27 27 LYS B 237 LYS B 242 1 6 HELIX 28 28 LYS B 242 ALA B 258 1 17 SHEET 1 AA 6 LYS A 32 LEU A 36 0 SHEET 2 AA 6 HIS A 5 ILE A 9 1 N PHE A 6 O LYS A 32 SHEET 3 AA 6 VAL A 74 GLU A 79 1 N ILE A 75 O VAL A 7 SHEET 4 AA 6 ILE A 97 HIS A 103 1 N ALA A 98 O VAL A 74 SHEET 5 AA 6 LYS A 200 THR A 205 1 N VAL A 201 O GLY A 100 SHEET 6 AA 6 LYS A 227 VAL A 231 1 N LYS A 227 O TYR A 202 SHEET 1 AB 2 GLU A 132 THR A 137 0 SHEET 2 AB 2 THR A 143 LYS A 148 -1 N LYS A 148 O GLU A 132 SHEET 1 BA 6 LYS B 32 LEU B 36 0 SHEET 2 BA 6 HIS B 5 ILE B 9 1 N PHE B 6 O LYS B 32 SHEET 3 BA 6 VAL B 74 GLU B 79 1 N ILE B 75 O VAL B 7 SHEET 4 BA 6 ILE B 97 HIS B 103 1 N ALA B 98 O VAL B 74 SHEET 5 BA 6 LYS B 200 TRP B 204 1 N VAL B 201 O GLY B 100 SHEET 6 BA 6 LYS B 227 GLN B 230 1 N LYS B 227 O TYR B 202 SHEET 1 BB 2 GLU B 132 THR B 137 0 SHEET 2 BB 2 THR B 143 LYS B 148 -1 N LYS B 148 O GLU B 132 SITE 1 AC1 2 SER A 80 CYS A 81 SITE 1 AC2 3 SER B 80 CYS B 81 MET B 147 CRYST1 106.600 106.600 189.000 90.00 90.00 90.00 P 41 21 2 16 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 0.009381 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005291 0.00000