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- PDB-7br1: Hydroxynitrile lyase from Parafontaria laminate complexed with be... -

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Basic information

Entry
Database: PDB / ID: 7br1
TitleHydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization
ComponentsHydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / millipede
Function / homologybenzaldehyde / THIOCYANATE ION
Function and homology information
Biological speciesParafontaria laminata (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 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 prepared by cocrystallization
Authors: Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y.
History
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Source and taxonomy / Structure summary / Category: entity_src_gen / struct
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title
Revision 1.2Nov 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 1.3Nov 20, 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)37,02712
Polymers36,2462
Non-polymers78110
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-39 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.934, 32.763, 84.632
Angle α, β, γ (deg.)90.000, 102.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hydroxynitrile lyase


Mass: 18123.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parafontaria laminata / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: potassium thiocyanate, sodium acetate pH 5.5, 10% w/v PEG 8000, 10% w/v 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 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→82.517 Å / Num. all: 84891 / Num. obs: 84891 / % possible obs: 100 % / Redundancy: 6.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Rsym value: 0.053 / Net I/av σ(I): 10.5 / Net I/σ(I): 18.1 / Num. measured all: 556553
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
1.25-1.326.30.8390.977278123240.3620.9160.8392.1100
1.32-1.46.70.5171.577813116600.2150.5610.5173.5100
1.4-1.496.40.3082.570231109680.1310.3350.3085.4100
1.49-1.616.60.1864.267478101580.0770.2020.1868.8100
1.61-1.776.70.1156.66315794230.0480.1250.11513.5100
1.77-1.986.60.06910.85602385460.0290.0750.06921.3100
1.98-2.286.90.04515.85211975690.0190.0490.04533.5100
2.28-2.86.40.03519.54075563900.0150.0380.03541.699.9
2.8-3.956.80.02524.73390250170.010.0270.02560.4100
3.95-41.9456.30.022251779728360.010.0250.02265.799.7

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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: 1.25→41.98 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.409 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.037
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1475 4296 5.1 %RANDOM
Rwork0.1403 ---
obs0.1407 80582 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.7 Å2 / Biso mean: 13.322 Å2 / Biso min: 8.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.25→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 52 459 3055
Biso mean--20.48 28.96 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132732
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172335
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6573739
X-RAY DIFFRACTIONr_angle_other_deg1.3921.5725468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0885340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35924.504131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77515389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.973155
X-RAY DIFFRACTIONr_chiral_restr0.0630.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.151 315 -
Rwork0.142 5900 -
all-6215 -
obs--99.84 %

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