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- PDB-7yct: HYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexe... -

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Basic information

Entry
Database: PDB / ID: 7yct
TitleHYDROXYNITRILE LYASE FROM THE MILLIPEDE, Oxidus gracilis complexed with (R)-2-Chloromandelonitrile
ComponentsHydroxynitrile lyase
KeywordsLYASE
Function / homologylyase activity / Chem-IJ5 / 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

Downloads & links

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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)83,48220
Polymers81,5364
Non-polymers1,94616
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-105 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.790, 123.790, 129.500
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-433-

HOH

21B-434-

HOH

31B-435-

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-IJ5 / (2~{R})-2-(2-chlorophenyl)-2-oxidanyl-ethanenitrile / (R)-2-chloromandelonitrile


Mass: 167.592 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H6ClNO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS (pH 5.5), 2.0 M ammonium sulfate incubated in 25% (v/v) glycerol with a drop of (R)-2-Chlorobenzaldehyde, and soaked with 2 M 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→61.9 Å / Num. obs: 74391 / % possible obs: 99.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.4
Reflection shellResolution: 2.01→2.05 Å / Rmerge(I) obs: 0.294 / Num. unique obs: 4580

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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→53.66 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.988 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1996 3627 4.876 %
Rwork0.171 70753 -
all0.172 --
obs-74380 99.21 %
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: 29.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.007 Å20.004 Å20 Å2
2--0.007 Å2-0 Å2
3----0.024 Å2
Refinement stepCycle: LAST / Resolution: 2.01→53.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 121 474 5650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0115335
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164525
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.6587288
X-RAY DIFFRACTIONr_angle_other_deg0.5751.55310632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7085650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.3871018
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09510787
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.82910255
X-RAY DIFFRACTIONr_chiral_restr0.080.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
X-RAY DIFFRACTIONr_nbd_refined0.2250.2960
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24325
X-RAY DIFFRACTIONr_nbtor_refined0.180.22530
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2411
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1980.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0660.210
X-RAY DIFFRACTIONr_nbd_other0.1220.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.220
X-RAY DIFFRACTIONr_mcbond_it2.832.9682606
X-RAY DIFFRACTIONr_mcbond_other2.8292.9682606
X-RAY DIFFRACTIONr_mcangle_it3.764.4373254
X-RAY DIFFRACTIONr_mcangle_other3.7594.4373255
X-RAY DIFFRACTIONr_scbond_it4.4973.4522729
X-RAY DIFFRACTIONr_scbond_other4.3263.4232710
X-RAY DIFFRACTIONr_scangle_it6.1494.9844034
X-RAY DIFFRACTIONr_scangle_other5.9734.9364005
X-RAY DIFFRACTIONr_lrange_it7.66240.3155883
X-RAY DIFFRACTIONr_lrange_other7.58139.0895772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.2682790.2285258X-RAY DIFFRACTION99.7298
2.06-2.1160.2562390.2135093X-RAY DIFFRACTION99.9812
2.116-2.1780.2432420.2025000X-RAY DIFFRACTION99.9809
2.178-2.2450.2142600.1894840X-RAY DIFFRACTION99.9608
2.245-2.3180.2122350.184674X-RAY DIFFRACTION99.8982
2.318-2.3990.2082110.1744549X-RAY DIFFRACTION99.8532
2.399-2.490.2042450.1694369X-RAY DIFFRACTION99.7837
2.49-2.5910.2162220.1764190X-RAY DIFFRACTION99.7062
2.591-2.7060.2171850.1764044X-RAY DIFFRACTION99.5996
2.706-2.8380.222080.1773839X-RAY DIFFRACTION99.5327
2.838-2.9910.1981770.1773663X-RAY DIFFRACTION99.3532
2.991-3.1720.2291700.1883477X-RAY DIFFRACTION98.9957
3.172-3.390.1991770.1873216X-RAY DIFFRACTION98.9501
3.39-3.660.2111350.1743041X-RAY DIFFRACTION98.6335
3.66-4.0080.1971480.1612758X-RAY DIFFRACTION98.3085
4.008-4.4780.1451180.1272512X-RAY DIFFRACTION97.7695
4.478-5.1640.1461330.1212175X-RAY DIFFRACTION97.4251
5.164-6.310.171910.1541851X-RAY DIFFRACTION96.9546
6.31-8.8630.1841030.1551413X-RAY DIFFRACTION95.9494

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