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- PDB-7yax: HYDROXYNITRILE LYASE FROM THE MILLIPEDE, -

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Basic information

Entry
Database: PDB / ID: 7yax
TitleHYDROXYNITRILE LYASE FROM THE MILLIPEDE,
ComponentsHydroxynitrile lyase
KeywordsLYASE
Function / homologylyase activity / Hydroxynitrile lyase
Function and homology information
Biological speciesOxidus gracilis (arthropod)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChaikaew, S. / Watanabe, Y. / Zheng, D. / Motojima, F. / Asano, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER1102 Japan
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
Japan Society for the Promotion of Science (JSPS)22H00361 Japan
CitationJournal: Chembiochem / Year: 2024
Title: Structure-Based Site-Directed Mutagenesis of Hydroxynitrile Lyase from Cyanogenic Millipede, Oxidus gracilis for Hydrocyanation and Henry Reactions.
Authors: Chaikaew, S. / Watanabe, Y. / Zheng, D. / Motojima, F. / Yamaguchi, T. / Asano, Y.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxynitrile lyase
B: Hydroxynitrile lyase
C: Hydroxynitrile lyase
D: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,83020
Polymers81,5364
Non-polymers1,29516
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10450 Å2
ΔGint-258 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.630, 123.630, 129.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-492-

HOH

21C-505-

HOH

31C-517-

HOH

41C-518-

HOH

51C-522-

HOH

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Components

#1: Protein
Hydroxynitrile lyase


Mass: 20383.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxidus gracilis (arthropod) / Gene: OgraHNL / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5XCT7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.49 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS (pH 5.5), 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→64.57 Å / Num. obs: 595005 / % possible obs: 99.58 % / Redundancy: 8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.6
Reflection shellResolution: 2.01→2.05 Å / Rmerge(I) obs: 0.221 / Num. unique obs: 4547

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFE

6kfe


Resolution: 2.01→39.969 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.225 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 3626 4.882 %RANDOM
Rwork0.1453 70642 --
all0.147 ---
obs-74268 99.578 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.132 Å2
Baniso -1Baniso -2Baniso -3
1-0.374 Å20.187 Å20 Å2
2--0.374 Å2-0 Å2
3----1.213 Å2
Refinement stepCycle: LAST / Resolution: 2.01→39.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 64 865 6008
Refine LS restraintsType: r_lrange_other / Dev ideal: 6.104 / Dev ideal target: 27.828 / Number: 6049
LS refinement shellResolution: 6.279→8.772 Å
RfactorNum. reflection% reflection
Rfree0.229 107 -
Rwork0.189 1459 -
obs--100 %

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