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- PDB-7bpo: Hydroxynitrile lyase from Parafonteria laminate complexed with be... -

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Basic information

Entry
Database: PDB / ID: 7bpo
TitleHydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde
ComponentsHydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / millipede
Function / homologybenzaldehyde
Function and homology information
Biological speciesParafontaria falcifera (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsNuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER1102 Japan
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
CitationJournal: To Be Published
Title: Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde
Authors: Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y.
History
DepositionMar 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7576
Polymers36,3612
Non-polymers3964
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-29 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.304, 33.130, 72.018
Angle α, β, γ (deg.)90.000, 106.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydroxynitrile lyase


Mass: 18180.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parafontaria falcifera (arthropod) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffleT7
#2: Chemical ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: potassium thiocyanate, sodium acetate PEG 8000 and PEG 1000, benzaldehyde

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→69.168 Å / Num. all: 63260 / Num. obs: 63260 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Rsym value: 0.082 / Net I/av σ(I): 4.1 / Net I/σ(I): 11.7 / Num. measured all: 420603
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.37-1.445.90.7311.14807180850.3220.8010.7312.385.5
1.44-1.536.90.461.76060187240.1870.4970.463.896.9
1.53-1.646.60.2882.65463582190.120.3130.2885.697
1.64-1.7770.1873.95383977140.0760.2020.1878.397.6
1.77-1.946.60.1255.44764571770.0530.1360.12511.998.2
1.94-2.176.80.0974463865210.0370.0980.0916.698.9
2.17-2.56.60.0767.73843258050.0320.0820.07619.699.1
2.5-3.066.80.0697.93378749420.0290.0750.06923.399.4
3.06-4.336.40.0638.32485738610.0270.0690.06325.899.8
4.33-34.866.40.06281409822120.0260.0670.06225.899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JHC

6jhc


Resolution: 1.37→34.88 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.63 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1761 3169 5 %RANDOM
Rwork0.1589 ---
obs0.1598 60087 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 50.32 Å2 / Biso mean: 17.066 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.37→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 28 434 3016
Biso mean--32.37 32.3 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172312
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6543692
X-RAY DIFFRACTIONr_angle_other_deg1.3791.5725415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01424.646127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85515386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.795154
X-RAY DIFFRACTIONr_chiral_restr0.0610.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
LS refinement shellResolution: 1.37→1.406 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.15 168 -
Rwork0.136 3467 -
all-3635 -
obs--75.95 %

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