| content |
HEADER COMPLEX (LYASE/PEPTIDE) 15-MAY-96 1YAS
TITLE HYDROXYNITRILE LYASE COMPLEXED WITH HISTIDINE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HYDROXYNITRILE LYASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: OXYNITRILE LYASE;
COMPND 5 EC: 4.2.1.39;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: HISTIDINE;
COMPND 9 CHAIN: B
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HEVEA BRASILIENSIS;
SOURCE 3 ORGANISM_COMMON: RUBBER TREE;
SOURCE 4 ORGAN: LEAF;
SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 6 EXPRESSION_SYSTEM_PLASMID: BHIL-D2;
SOURCE 7 EXPRESSION_SYSTEM_GENE: HNL;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES
KEYWDS OXYNITRILASE, CYANOGENESIS, CYANHYDRIN FORMATION, LYASE,
KEYWDS 2 COMPLEX (LYASE/PEPTIDE)
EXPDTA X-RAY DIFFRACTION
AUTHOR U.G.WAGNER,C.KRATKY
REVDAT 1 16-JUN-97 1YAS 0
JRNL AUTH U.G.WAGNER,M.HASSLACHER,H.GRIENGL,H.SCHWAB,C.KRATKY
JRNL TITL MECHANISM OF CYANOGENESIS: THE CRYSTAL STRUCTURE OF
JRNL TITL 2 HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS
JRNL REF STRUCTURE (LONDON) V. 4 811 1996
JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 2005
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH M.HASSLACHER,C.KRATKY,H.GRIENGL,H.SCHWAB,
REMARK 1 AUTH 2 S.D.KOHLWEIN
REMARK 1 TITL HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS:
REMARK 1 TITL 2 MOLECULAR CHARACTERIZATION AND MECHANISM OF ENZYME
REMARK 1 TITL 3 CATALYSIS
REMARK 1 REF PROTEINS: STRUCT.,FUNCT., V. 27 438 1997
REMARK 1 REF 2 GENET.
REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 0867
REMARK 1 REFERENCE 2
REMARK 1 AUTH U.G.WAGNER,M.SCHALL,M.HAYN,M.HASSLACHER,H.SCHWAB,
REMARK 1 AUTH 2 H.S.GRIENGL,C.KRATKY
REMARK 1 TITL CRYSTALLIZATION OF A HYDROXYNITRILE LYASE
REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 52 591 1996
REMARK 1 REFN ASTM ABCRE6 DK ISSN 0907-4449 0766
REMARK 1 REFERENCE 3
REMARK 1 AUTH M.HASSLACHER,M.SCHALL,M.HAYN,H.GRIENGL,
REMARK 1 AUTH 2 S.D.KOHLWEIN,H.SCHWAB
REMARK 1 TITL MOLECULAR CLONING OF THE FULL-LENGTH CDNA OF
REMARK 1 TITL 2 (S)-HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS.
REMARK 1 TITL 3 FUNCTIONAL EXPRESSION IN ESCHERICHIA COLI AND
REMARK 1 TITL 4 SACCHAROMYCES CEREVISIAE AND IDENTIFICATION OF AN
REMARK 1 TITL 5 ACTIVE SITE RESIDUE
REMARK 1 REF J.BIOL.CHEM. V. 271 5884 1996
REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 0071
REMARK 2
REMARK 2 RESOLUTION. 1.9 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) : 1.9
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.
REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.0
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 76.7
REMARK 3 NUMBER OF REFLECTIONS : 20547
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : FREE-R
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.199
REMARK 3 FREE R VALUE : 0.241
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.
REMARK 3 FREE R VALUE TEST SET COUNT : 2030
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) : 1.9
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.68
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1230
REMARK 3 BIN R VALUE (WORKING SET) : 0.338
REMARK 3 BIN FREE R VALUE : 0.381
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.58
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 139
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 : 2057
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 16
REMARK 3 SOLVENT ATOMS : 77
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 15.296
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.75
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.856
REMARK 3 B22 (A**2) : 1.298
REMARK 3 B33 (A**2) : 1.558
REMARK 3 B12 (A**2) : 0.000
REMARK 3 B13 (A**2) : 0.000
REMARK 3 B23 (A**2) : 0.000
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) : 15.
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) : 0.018
REMARK 3 BOND ANGLES (DEGREES) : 2.990
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.471
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.388
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 : PARAM19X.SOL
REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO
REMARK 3 TOPOLOGY FILE 2 : TOPH19X.SOL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1YAS COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-MAY-1995
REMARK 200 TEMPERATURE (KELVIN) : 120
REMARK 200 PH : 7.5
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 : X31
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.92
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 : 24031
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90
REMARK 200 RESOLUTION RANGE LOW (A) : 15.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4
REMARK 200 DATA REDUNDANCY : 5.0
REMARK 200 R MERGE (I) : 0.073
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.0
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) : 1.93
REMARK 200 COMPLETENESS FOR SHELL (%) : 67.8
REMARK 200 DATA REDUNDANCY IN SHELL : 2.5
REMARK 200 R MERGE FOR SHELL (I) : 0.355
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.0
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR
REMARK 200 SOFTWARE USED: CCP4
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.8
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NATRIUM HEPES BUFFER
REMARK 280 PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES.
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,1/2+Z
REMARK 290 3555 -X,Y,1/2-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 1/2+X,1/2+Y,Z
REMARK 290 6555 1/2-X,1/2-Y,1/2+Z
REMARK 290 7555 1/2-X,1/2+Y,1/2-Z
REMARK 290 8555 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 64.11079
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.11079
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.85155
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.50779
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.85155
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.50779
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.11079
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.85155
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.50779
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.11079
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.85155
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.50779
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 HOH 575 LIES ON A SPECIAL POSITION.
REMARK 375 HOH 576 LIES ON A SPECIAL POSITION.
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. SOME OF THESE MAY BE ATOMS
REMARK 500 LOCATED ON SPECIAL POSITIONS IN THE CELL. ATOMS WITH
REMARK 500 NON-BLANK ALTERNATE LOCATION INDICATORS ARE NOT INCLUDED
REMARK 500 IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH 575 O HOH 575 3655 0.50
REMARK 500 O HOH 576 O HOH 576 3655 0.78
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 SITE_DESCRIPTION: BINDING SITE.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 1YAS A SWS P52704 1 - 1 NOT IN ATOMS LIST
DBREF 1YAS A 2 257 SWS P52704 HNL_HEVBR 2 257
DBREF 1YAS B 300 300 PDB 1YAS 1YAS 300 300
SEQRES 1 A 257 MET ALA PHE ALA HIS PHE VAL LEU ILE HIS THR ILE CYS
SEQRES 2 A 257 HIS GLY ALA TRP ILE TRP HIS LYS LEU LYS PRO LEU LEU
SEQRES 3 A 257 GLU ALA LEU GLY HIS LYS VAL THR ALA LEU ASP LEU ALA
SEQRES 4 A 257 ALA SER GLY VAL ASP PRO ARG GLN ILE GLU GLU ILE GLY
SEQRES 5 A 257 SER PHE ASP GLU TYR SER GLU PRO LEU LEU THR PHE LEU
SEQRES 6 A 257 GLU ALA LEU PRO PRO GLY GLU LYS VAL ILE LEU VAL GLY
SEQRES 7 A 257 GLU SER CYS GLY GLY LEU ASN ILE ALA ILE ALA ALA ASP
SEQRES 8 A 257 LYS TYR CYS GLU LYS ILE ALA ALA ALA VAL PHE HIS ASN
SEQRES 9 A 257 SER VAL LEU PRO ASP THR GLU HIS CYS PRO SER TYR VAL
SEQRES 10 A 257 VAL ASP LYS LEU MET GLU VAL PHE PRO ASP TRP LYS ASP
SEQRES 11 A 257 THR THR TYR PHE THR TYR THR LYS ASP GLY LYS GLU ILE
SEQRES 12 A 257 THR GLY LEU LYS LEU GLY PHE THR LEU LEU ARG GLU ASN
SEQRES 13 A 257 LEU TYR THR LEU CYS GLY PRO GLU GLU TYR GLU LEU ALA
SEQRES 14 A 257 LYS MET LEU THR ARG LYS GLY SER LEU PHE GLN ASN ILE
SEQRES 15 A 257 LEU ALA LYS ARG PRO PHE PHE THR LYS GLU GLY TYR GLY
SEQRES 16 A 257 SER ILE LYS LYS ILE TYR VAL TRP THR ASP GLN ASP GLU
SEQRES 17 A 257 ILE PHE LEU PRO GLU PHE GLN LEU TRP GLN ILE GLU ASN
SEQRES 18 A 257 TYR LYS PRO ASP LYS VAL TYR LYS VAL GLU GLY GLY ASP
SEQRES 19 A 257 HIS LYS LEU GLN LEU THR LYS THR LYS GLU ILE ALA GLU
SEQRES 20 A 257 ILE LEU GLN GLU VAL ALA ASP THR TYR ASN
SEQRES 1 B 1 HIS
HET SO4 301 5
HETNAM SO4 SULFATE ION
FORMUL 3 SO4 O4 S1 2-
FORMUL 4 HOH *77(H2 O1)
HELIX 1 HA LYS A 21 ALA A 28 1 8
HELIX 2 HB SER A 53 LEU A 68 1 16
HELIX 3 HC CYS A 81 CYS A 94 1 14
HELIX 4 HD1 SER A 115 PHE A 125 1 BELONGS TO THE CAP DOMAIN 11
HELIX 5 HD2 GLY A 149 LEU A 157 1 BELONGS TO THE CAP DOMAIN 9
HELIX 6 HD3 GLY A 162 THR A 173 1 BELONGS TO THE CAP DOMAIN 12
HELIX 7 HD PHE A 179 LYS A 185 1 7
HELIX 8 HE LEU A 211 TYR A 222 1 12
HELIX 9 HF LYS A 236 TYR A 256 1 21
SHEET 1 S1 6 ALA A 4 ILE A 9 0
SHEET 2 S1 6 LYS A 32 LEU A 36 1
SHEET 3 S1 6 SER A 53 LEU A 68 -1
SHEET 4 S1 6 LYS A 96 ASN A 104 -1
SHEET 5 S1 6 LYS A 198 TRP A 203 1
SHEET 6 S1 6 LYS A 226 VAL A 230 1
SHEET 1 S2 3 THR A 132 LYS A 138 0
SHEET 2 S2 3 LYS A 141 LYS A 147 -1
SHEET 3 S2 3 GLY A 176 LEU A 178 -1
SITE 1 CAT 1 HIS A 235
CRYST1 47.703 109.010 128.226 90.00 90.00 90.00 C 2 2 21 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 0.020963 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009173 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007799 0.00000 |