10 20 30 40 50 60 70 80 1E89 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 18-SEP-00 1E89
TITLE ON THE MECHANISM OF CYANOGENESIS CATALYZED BY TITLE 2 HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA. CRYSTAL TITLE 3 STRUCTURE OF ACTIVE SITE MUTANT SER80ALA IN COMPLEX WITH TITLE 4 ACETONE CYANOHYDRIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYNITRILE LYASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: (S)-ACETONE-CYANOHYDRIN LYASE, COMPND 5 (S)-HYDROXYNITRILASE; COMPND 6 EC: 4.2.1.37; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES
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
KEYWDS LYASE, HYDROXYNITRILE LYASE, ACTIVE SITE MUTANT, ACETONE KEYWDS 2 CYANOHYDRIN COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR H.LAUBLE,B.MIEHLICH,S.FOERSTER,H.WAJANT,F.EFFENBERGER
REVDAT 2 24-FEB-09 1E89 1 VERSN REVDAT 1 17-AUG-01 1E89 0
JRNL AUTH H.LAUBLE,B.MIEHLICH,S.FOERSTER,H.WAJANT, JRNL AUTH 2 F.EFFENBERGER JRNL TITL MECHANISTIC ASPECTS OF CYANOGENESIS FROM JRNL TITL 2 ACTIVE-SITE MUTANT SER80ALA OF HYDROXYNITRILE JRNL TITL 3 LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH JRNL TITL 4 ACETONE CYANOHYDRIN JRNL REF PROTEIN SCI. V. 10 1015 2001 JRNL REFN ISSN 0961-8368 JRNL PMID 11316882 JRNL DOI 10.1110/PS.01301
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.LAUBLE,S.FOERSTER,B.MIEHLICH,H.WAJANT, REMARK 1 AUTH 2 F.EFFENBERGER REMARK 1 TITL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT REMARK 1 TITL 2 ESCULENTA IN COMPLEX WITH SUBSTRATES ACETONE AND REMARK 1 TITL 3 CHLOROACETONE: IMPLICATIONS FOR THE MECHANISM OF REMARK 1 TITL 4 CYANOGENESIS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 57 194 2001 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 11173464 REMARK 1 DOI 10.1107/S0907444900015766
REMARK 2 REMARK 2 RESOLUTION. 2.1 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.00 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.001000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 60467 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 SET) : 0.180 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.0 REMARK 3 FREE R VALUE TEST SET COUNT : 6024 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8746 REMARK 3 BIN R VALUE (WORKING SET) : 0.229 REMARK 3 BIN FREE R VALUE : 0.249 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.8 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 951 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.008 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4176 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 426 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.00 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.8 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.0 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.13 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.58 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.33 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.53 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.42 ; 2.50 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 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1E89 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-SEP-00. REMARK 100 THE PDBE ID CODE IS EBI-5364.
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 : 4.80 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 : 63336 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 96.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1DWO REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.5 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NACITRAT, PH 4.8, REMARK 280 6% PEG8000, 28% MPD
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 94.07500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.09000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.03750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.09000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.09000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 141.11250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.09000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.09000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.03750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.09000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.09000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 141.11250 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 94.07500 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 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 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS 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 188.20000
REMARK 400 REMARK 400 COMPOUND REMARK 400 CHAIN A, B: CONTAINS ENGINEERED MUTATION S80A. REMARK 400 RESIDUES -4 TO 1 ARE CLONING ARTEFACTS
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 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. = 5.0 DEGREES REMARK 500 TRP A 19 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP A 19 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 HIS A 31 CB - CG - ND1 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 HIS A 103 CB - CG - ND1 ANGL. DEV. = 8.3 DEGREES REMARK 500 TRP A 128 CD1 - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP A 128 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 175 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ILE A 198 CA - CB - CG1 ANGL. DEV. = -13.7 DEGREES REMARK 500 ILE A 198 CA - CB - CG2 ANGL. DEV. = 13.0 DEGREES REMARK 500 TRP A 204 CD1 - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TRP A 204 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 TRP A 218 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP A 218 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 HIS A 236 CB - CG - ND1 ANGL. DEV. = 9.4 DEGREES REMARK 500 HIS A 248 CB - CG - ND1 ANGL. DEV. = 9.0 DEGREES REMARK 500 THR B 3 N - CA - CB ANGL. DEV. = -11.5 DEGREES REMARK 500 HIS B 14 CB - CG - ND1 ANGL. DEV. = 8.2 DEGREES REMARK 500 TRP B 17 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 ILE B 18 CB - CA - C ANGL. DEV. = -12.8 DEGREES REMARK 500 TRP B 19 CD1 - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 TRP B 19 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 28 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 92 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 92 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 HIS B 103 CB - CG - ND1 ANGL. DEV. = 8.4 DEGREES REMARK 500 TRP B 128 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG B 155 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 155 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 THR B 163 N - CA - CB ANGL. DEV. = -12.3 DEGREES REMARK 500 ARG B 175 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ILE B 198 CA - CB - CG1 ANGL. DEV. = -17.0 DEGREES REMARK 500 ILE B 198 CA - CB - CG2 ANGL. DEV. = 15.3 DEGREES REMARK 500 TRP B 204 CD1 - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 TRP B 204 CE2 - CD2 - CG ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG B 217 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 TRP B 218 CD1 - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 TRP B 218 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 HIS B 236 CB - CG - ND1 ANGL. DEV. = 8.9 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 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 -23.73 80.48 REMARK 500 ALA A 80 -109.27 43.41 REMARK 500 ASP A 109 -168.56 -126.72 REMARK 500 ARG A 129 -115.16 55.31 REMARK 500 ILE A 210 -48.68 -131.49 REMARK 500 TYR A 223 85.56 -154.93 REMARK 500 CYS B 13 -18.29 78.56 REMARK 500 ALA B 80 -107.65 40.82 REMARK 500 ASP B 109 -168.48 -126.25 REMARK 500 ARG B 129 -108.85 55.69 REMARK 500 ILE B 210 -47.94 -133.66 REMARK 500 TYR B 223 89.45 -154.11 REMARK 500 LYS B 242 45.62 -140.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR B 3 45.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DWO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT REMARK 900 ESCULENTA INCOMPLEX WITH SUBSTRATES ACETONE AND REMARK 900 CHLOROACETONE:IMPLICATIONS FOR THEMECHANISM OF REMARK 900 CYANOGENESIS REMARK 900 RELATED ID: 1DWP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT REMARK 900 ESCULENTA AT 2.2 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 1DWQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HYDROXYNITRILE LYASE FROM MANIHOT REMARK 900 ESCULENTA INCOMPLEX WITH SUBSTRATES ACETONE AND REMARK 900 CHLOROACETONE:IMPLICATIONS FOR THEMECHANISM OF REMARK 900 CYANOGENESIS
DBREF 1E89 A -4 1 PDB 1E89 1E89 -4 1 DBREF 1E89 A 2 258 UNP P52705 HNL_MANES 1 257 DBREF 1E89 B -4 1 PDB 1E89 1E89 -4 1 DBREF 1E89 B 2 258 UNP P52705 HNL_MANES 1 257
SEQADV 1E89 ALA A 80 UNP P52705 SER 79 ENGINEERED MUTATION SEQADV 1E89 ALA B 80 UNP P52705 SER 79 ENGINEERED MUTATION
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 ALA 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 ALA 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
FORMUL 3 HOH *426(H2 O1)
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 LEU A 158 1 9 HELIX 9 9 THR A 163 MET A 174 1 12 HELIX 10 10 PHE A 180 GLN A 186 1 7 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 LEU B 158 1 9 HELIX 23 23 THR B 163 MET B 174 1 12 HELIX 24 24 PHE B 180 GLN B 186 1 7 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 A 6 LYS A 32 LEU A 36 0 SHEET 2 A 6 HIS A 5 ILE A 9 1 N PHE A 6 O LYS A 32 SHEET 3 A 6 VAL A 74 GLU A 79 1 N ILE A 75 O VAL A 7 SHEET 4 A 6 ILE A 97 HIS A 103 1 N ALA A 98 O VAL A 74 SHEET 5 A 6 LYS A 200 TRP A 204 1 N VAL A 201 O GLY A 100 SHEET 6 A 6 LYS A 227 GLN A 230 1 N LYS A 227 O TYR A 202 SHEET 1 B 2 GLU A 132 THR A 137 0 SHEET 2 B 2 THR A 143 LYS A 148 -1 N LYS A 148 O GLU A 132 SHEET 1 C 6 LYS B 32 LEU B 36 0 SHEET 2 C 6 HIS B 5 ILE B 9 1 N PHE B 6 O LYS B 32 SHEET 3 C 6 VAL B 74 GLU B 79 1 N ILE B 75 O VAL B 7 SHEET 4 C 6 ILE B 97 HIS B 103 1 N ALA B 98 O VAL B 74 SHEET 5 C 6 LYS B 200 TRP B 204 1 N VAL B 201 O GLY B 100 SHEET 6 C 6 LYS B 227 GLN B 230 1 N LYS B 227 O TYR B 202 SHEET 1 D 2 GLU B 132 THR B 137 0 SHEET 2 D 2 THR B 143 LYS B 148 -1 N LYS B 148 O GLU B 132
CRYST1 106.180 106.180 188.150 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 0.009418 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009418 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005315 0.00000