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- PDB-3c6z: HNL from Hevea brasiliensis to atomic resolution -

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Basic information

Entry
Database: PDB / ID: 3c6z
TitleHNL from Hevea brasiliensis to atomic resolution
ComponentsHydroxynitrilase
KeywordsLYASE / atomic resolution / hydroxynitril lyase / catalysis / protonation state / ab initio calculations / substrate binding
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
BETA-MERCAPTOETHANOL / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement/rigid body placement / Resolution: 1.05 Å
AuthorsSchmidt, A.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis
Authors: Schmidt, A. / Gruber, K. / Kratky, C. / Lamzin, V.S.
#1: Journal: Protein Sci. / Year: 1999
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: 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.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxynitrilase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8918
Polymers29,2631
Non-polymers6297
Water10,953608
1
A: Hydroxynitrilase
hetero molecules

A: Hydroxynitrilase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,78216
Polymers58,5252
Non-polymers1,25714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area4500 Å2
ΔGint-97.8 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.243, 106.373, 128.309
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-3009-

HOH

21A-3039-

HOH

31A-3177-

HOH

41A-3317-

HOH

51A-3545-

HOH

61A-3580-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hydroxynitrilase / / (S)-acetone-cyanohydrin lyase / (S)-hydroxynitrile lyase / Oxynitrilase


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 / Plasmid: BHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: P52704, EC: 4.1.2.37

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Non-polymers , 5 types, 615 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG400, 2M ammonium sulphate, 0.1M Hepes-Na, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2005 / Details: mirror
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. all: 140831 / Num. obs: 140831 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26
Reflection shellResolution: 1.05→1.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1721 / % possible all: 50

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMAC(rigid body)phasing
RefinementMethod to determine structure: molecular replacement/rigid body placement
Starting model: PDB ENTRY 1QJ4

1qj4


Resolution: 1.05→30 Å / Num. parameters: 25764 / Num. restraintsaints: 31662
Cross valid method: FREE R initially, final refinement against all data
σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER / Details: full anisotropic refinement applied
RfactorNum. reflection% reflectionSelection details
all0.1087 140831 --
obs-140831 100 %-
Rfree---RANDOM
Displacement parametersBiso mean: 11 Å2
Refine analyzeNum. disordered residues: 38 / Occupancy sum hydrogen: 2040.7 / Occupancy sum non hydrogen: 2654.25
Refinement stepCycle: LAST / Resolution: 1.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4415 0 24 621 5060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0285
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.101
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.099

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