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- PDB-1qj4: HYDROXYNITRILE-LYASE FROM HEVEA BRASILIENSIS AT ATOMIC RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1qj4
TitleHYDROXYNITRILE-LYASE FROM HEVEA BRASILIENSIS AT ATOMIC RESOLUTION
ComponentsHYDROXYNITRILE LYASE
KeywordsLYASE / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN FORMATION
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHEVEA BRASILIENSIS (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGugganig, M. / Gruber, K. / Kratky, C.
Citation
Journal: Biol.Chem. / Year: 1999
Title: Atomic Resolution Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
Authors: Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C.
#1: Journal: Protein Sci. / Year: 2000
Title: Three-Dimensional Structures of Enzyme-Substrate Complexes of the Hydroxynitrile Lyase from Hevea Brasiliensis
Authors: Zuegg, J. / Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C.
#2: Journal: Structure / Year: 1996
Title: Mechanism of Cyanogenesis: The Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
Authors: Wagner, U.G. / Hasslacher, M. / Griengl, H. / Schwab, H. / Kratky, C.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization of a Hydroxynitrile Lyase
Authors: Wagner, U.G. / Schall, M. / Hayn, M. / Hasslacher, M. / Schwab, H. / Griengl, H.S. / Kratky, C.
#4: Journal: J.Biol.Chem. / Year: 1996
Title: Molecular Cloning of the Full-Length Cdna of (S)-Hydroxynitrile Lyase from Hevea Brasiliensis. Functional Expression in Escherichia Coli and Saccharomyces Cerevisiae and Identification of an Active Site Residue
Authors: Hasslacher, M. / Schall, M. / Hayn, M. / Griengl, H. / Kohlwein, S.D. / Schwab, H.
History
DepositionJun 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: DSSP
Remark 700 SHEET DETERMINATION METHOD: DSSP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7396
Polymers29,2631
Non-polymers4765
Water9,908550
1
A: HYDROXYNITRILE LYASE
hetero molecules

A: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,47812
Polymers58,5252
Non-polymers95310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area1880 Å2
ΔGint-16.2 kcal/mol
Surface area23800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)47.287, 106.655, 128.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2138-

HOH

21A-2142-

HOH

31A-2230-

HOH

41A-2398-

HOH

51A-2462-

HOH

61A-2468-

HOH

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Components

#1: Protein HYDROXYNITRILE LYASE / OXYNITRILE LYASE


Mass: 29262.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEVEA BRASILIENSIS (rubber tree) / Gene: HNL / Organ: LEAF / Plasmid: BHIL-D2 / Gene (production host): HNL / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P52704, EC: 4.1.2.39
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.4
Details: 0.1 M NATRIUM HEPES BUFFER PH=7.4 2 % PEG 400, 2.0 M AMMONIUM SULFATE, ROOM-TEMP., pH 7.40

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 123339 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.065 / Net I/σ(I): 20.4
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.364 / % possible all: 92.3

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YAS

7yas


Resolution: 1.1→50 Å / Num. parameters: 24572 / Num. restraintsaints: 43482 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.043. RESIDUE SER-A80 IS OBSERVED IN A RAMACHANDRAN 'FORBIDDEN' REGION. THIS CONFORMATION IS FOUND IN ALL PREVIOUS HNL-STRUCTURES. ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.043. RESIDUE SER-A80 IS OBSERVED IN A RAMACHANDRAN 'FORBIDDEN' REGION. THIS CONFORMATION IS FOUND IN ALL PREVIOUS HNL-STRUCTURES. STRUCTURES OF OTHER MEMBERS OF THE ALPHA/BETA HYDROLASES FAMILY ALSO CONSISTENTLY SHOW THE EQUIVALENT RESIDUE (NUCLEOPHILE) IN SUCH A CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1437 6192 5 %RANDOM
all0.1158 123339 --
obs0.1149 -94.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 25 / Occupancy sum hydrogen: 2053 / Occupancy sum non hydrogen: 2629.75
Refinement stepCycle: LAST / Resolution: 1.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 26 550 2632
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.109
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.029
X-RAY DIFFRACTIONs_approx_iso_adps0.059

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