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- PDB-7ycd: HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis bound wi... -

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Basic information

Entry
Database: PDB / ID: 7ycd
TitleHYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis bound with (R)-(+)-ALPHA-HYDROXYBENZENE-ACETONITRILE
ComponentsHydroxynitrile lyase
KeywordsLYASE
Function / homologylyase activity / (2R)-hydroxy(phenyl)ethanenitrile / 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
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 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 13, 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)83,17718
Polymers81,5364
Non-polymers1,64214
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-132 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.430, 123.430, 129.870
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
11A-384-

HOH

21A-385-

HOH

31A-386-

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-MXN / (2R)-hydroxy(phenyl)ethanenitrile / (R)-mandelonitrile


Mass: 133.147 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H7NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS, 2.0 M ammonium sulfate, incubated in 25% (v/v) glycerol with a drop of BA and 2M potassium cyanide

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→64.94 Å / Num. obs: 74395 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.2
Reflection shellResolution: 2.01→2.05 Å / Rmerge(I) obs: 0.846 / Num. unique obs: 4496

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Processing

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

6kfe


Resolution: 2.01→40.435 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.422 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.233 3640 4.896 %
Rwork0.2019 70710 -
all0.203 --
obs-74350 99.458 %
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: 42.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.782 Å20.391 Å20 Å2
2--0.782 Å2-0 Å2
3----2.538 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 110 342 5510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0115349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164511
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.667317
X-RAY DIFFRACTIONr_angle_other_deg0.5261.55310609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6665656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.2621016
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71610777
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.15910258
X-RAY DIFFRACTIONr_chiral_restr0.0690.2794
X-RAY DIFFRACTIONr_chiral_restr_other0.020.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021024
X-RAY DIFFRACTIONr_nbd_refined0.2150.21015
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24395
X-RAY DIFFRACTIONr_nbtor_refined0.180.22544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2329
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0990.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.213
X-RAY DIFFRACTIONr_nbd_other0.1840.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0780.210
X-RAY DIFFRACTIONr_mcbond_it3.5014.4772618
X-RAY DIFFRACTIONr_mcbond_other3.5014.4772618
X-RAY DIFFRACTIONr_mcangle_it4.7516.6963270
X-RAY DIFFRACTIONr_mcangle_other4.7516.6963271
X-RAY DIFFRACTIONr_scbond_it4.5374.8522731
X-RAY DIFFRACTIONr_scbond_other4.3374.8152707
X-RAY DIFFRACTIONr_scangle_it6.3687.1174045
X-RAY DIFFRACTIONr_scangle_other6.1717.0634010
X-RAY DIFFRACTIONr_lrange_it7.74857.0795834
X-RAY DIFFRACTIONr_lrange_other7.72556.6025756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.3452780.3365093X-RAY DIFFRACTION97.2655
2.06-2.1160.3362370.3245048X-RAY DIFFRACTION98.9145
2.116-2.1780.3532480.3024921X-RAY DIFFRACTION99.0799
2.178-2.2440.2822530.284795X-RAY DIFFRACTION99.5072
2.244-2.3180.332330.264656X-RAY DIFFRACTION99.7959
2.318-2.3990.272140.2484532X-RAY DIFFRACTION99.8317
2.399-2.4890.2712420.2414350X-RAY DIFFRACTION99.9782
2.489-2.590.32140.234173X-RAY DIFFRACTION100
2.59-2.7050.2471920.224059X-RAY DIFFRACTION99.953
2.705-2.8360.2742110.2113837X-RAY DIFFRACTION100
2.836-2.9890.2191780.2073685X-RAY DIFFRACTION99.9482
2.989-3.1690.2681680.2213490X-RAY DIFFRACTION99.9454
3.169-3.3860.2361720.2093265X-RAY DIFFRACTION99.9709
3.386-3.6560.2531380.193056X-RAY DIFFRACTION100
3.656-4.0010.2241510.1782790X-RAY DIFFRACTION99.7626
4.001-4.4680.1741210.1422547X-RAY DIFFRACTION99.8503
4.468-5.1490.1781370.1382236X-RAY DIFFRACTION99.9158
5.149-6.2810.202950.1591909X-RAY DIFFRACTION99.7015
6.281-8.7770.1571050.1451448X-RAY DIFFRACTION98.8542

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