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- PDB-7ycb: HYDROXYNITRILE LYASE FROM THE MILLIPEDE -

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Basic information

Entry
Database: PDB / ID: 7ycb
TitleHYDROXYNITRILE LYASE FROM THE MILLIPEDE
ComponentsHydroxynitrile lyase
KeywordsLYASE
Function / homologylyase activity / benzaldehyde / 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 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

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)83,57527
Polymers81,5364
Non-polymers2,04023
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.160, 123.160, 130.140
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-397-

HOH

21B-398-

HOH

31B-399-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 362 molecules

#2: Chemical
ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 64.8 %
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% glycerol with a drop of benzaldehyde and 2 M potassium cyanide

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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: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→61.58 Å / Num. obs: 74529 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.9
Reflection shellResolution: 2.01→2.05 Å / Rmerge(I) obs: 0.069 / Num. unique obs: 4631

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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→49.396 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.101 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2349 3631 4.873 %
Rwork0.2061 70882 -
all0.208 --
obs-74513 99.893 %
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: 39.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.323 Å20.162 Å20 Å2
2--0.323 Å2-0 Å2
3----1.049 Å2
Refinement stepCycle: LAST / Resolution: 2.01→49.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5072 0 125 339 5536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0115357
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164538
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6557320
X-RAY DIFFRACTIONr_angle_other_deg0.5141.55210659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9235656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6371017
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69610793
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.5710259
X-RAY DIFFRACTIONr_chiral_restr0.0690.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021034
X-RAY DIFFRACTIONr_nbd_refined0.2190.21021
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24415
X-RAY DIFFRACTIONr_nbtor_refined0.180.22570
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2337
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.212
X-RAY DIFFRACTIONr_nbd_other0.1480.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.210
X-RAY DIFFRACTIONr_mcbond_it3.5034.0822612
X-RAY DIFFRACTIONr_mcbond_other3.5024.0822612
X-RAY DIFFRACTIONr_mcangle_it4.8076.1023260
X-RAY DIFFRACTIONr_mcangle_other4.8066.1023261
X-RAY DIFFRACTIONr_scbond_it4.634.4482745
X-RAY DIFFRACTIONr_scbond_other4.254.3812710
X-RAY DIFFRACTIONr_scangle_it6.1656.5184056
X-RAY DIFFRACTIONr_scangle_other5.9076.424003
X-RAY DIFFRACTIONr_lrange_it7.82453.0035872
X-RAY DIFFRACTIONr_lrange_other7.82752.5385803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.3582710.3475254X-RAY DIFFRACTION99.9277
2.06-2.1160.3412400.3175098X-RAY DIFFRACTION100
2.116-2.1780.322570.2924940X-RAY DIFFRACTION100
2.178-2.2450.2892470.2794831X-RAY DIFFRACTION99.9803
2.245-2.3180.3052340.2714649X-RAY DIFFRACTION99.9795
2.318-2.3990.2842160.2614535X-RAY DIFFRACTION100
2.399-2.490.292410.2394321X-RAY DIFFRACTION100
2.49-2.5910.2972080.2244183X-RAY DIFFRACTION100
2.591-2.7060.2611930.2254052X-RAY DIFFRACTION99.9764
2.706-2.8370.2362100.2033842X-RAY DIFFRACTION99.9507
2.837-2.990.2331790.2123675X-RAY DIFFRACTION99.9741
2.99-3.1710.2631700.2253472X-RAY DIFFRACTION100
3.171-3.3890.2461700.2113258X-RAY DIFFRACTION100
3.389-3.6590.2361360.193062X-RAY DIFFRACTION99.9687
3.659-4.0060.2011530.1762775X-RAY DIFFRACTION99.8976
4.006-4.4750.1641210.1422536X-RAY DIFFRACTION99.7747
4.475-5.1610.1831350.1482231X-RAY DIFFRACTION99.7891
5.161-6.3030.189940.1571884X-RAY DIFFRACTION99.5972
6.303-8.8420.1971040.1641461X-RAY DIFFRACTION99.4282

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