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- PDB-7f30: Crystal structure of OxdB E85A in complex with Z-2- (3-bromopheny... -

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Basic information

Entry
Database: PDB / ID: 7f30
TitleCrystal structure of OxdB E85A in complex with Z-2- (3-bromophenyl) propanal oxime
ComponentsPhenylacetaldoxime dehydratase
KeywordsLYASE / Aldoxime dehydratase / heme
Function / homologyphenylacetaldoxime dehydratase / phenylacetaldoxime dehydratase activity / Haem-containing dehydratase / Haem-containing dehydratase / metal ion binding / Z-2-(3-bromophenyl) propanal oxime / PROTOPORPHYRIN IX CONTAINING FE / Phenylacetaldoxime dehydratase
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMuraki, N. / Matsui, D. / Asano, Y. / Aono, S.
CitationJournal: J.Inorg.Biochem. / Year: 2022
Title: Crystal structural analysis of aldoxime dehydratase from Bacillus sp. OxB-1: Importance of surface residues in optimization for crystallization.
Authors: Matsui, D. / Muraki, N. / Chen, K. / Mori, T. / Ingram, A.A. / Oike, K. / Groger, H. / Aono, S. / Asano, Y.
History
DepositionJun 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylacetaldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5153
Polymers41,6711
Non-polymers8452
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-23 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.922, 64.685, 52.563
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phenylacetaldoxime dehydratase


Mass: 41670.863 Da / Num. of mol.: 1 / Mutation: E85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (strain OxB-1) (bacteria) / Strain: OxB-1 / Gene: oxd / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P82604, EC: 4.99.1.7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-0WQ / Z-2-(3-bromophenyl) propanal oxime


Mass: 228.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10BrNO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) polyethylene glycol 4,000, 0.1 M Tris pH8.5, and 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.91939 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91939 Å / Relative weight: 1
ReflectionResolution: 2→40.792 Å / Num. obs: 22681 / % possible obs: 99.73 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05767 / Rpim(I) all: 0.03633 / Rrim(I) all: 0.06835 / Net I/σ(I): 14.41
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5143 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 2264 / CC1/2: 0.827 / Rpim(I) all: 0.3174 / Rrim(I) all: 0.6058 / % possible all: 99.87

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a15

3a15


Resolution: 2→40.792 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 2063 4.79 %Random selection
Rwork0.1839 ---
obs0.1855 22675 96.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 55 72 2818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072848
X-RAY DIFFRACTIONf_angle_d0.9083893
X-RAY DIFFRACTIONf_dihedral_angle_d14.9521642
X-RAY DIFFRACTIONf_chiral_restr0.054405
X-RAY DIFFRACTIONf_plane_restr0.006496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.32311190.29392761X-RAY DIFFRACTION98
2.0465-2.09770.30561670.25582799X-RAY DIFFRACTION99
2.0977-2.15440.22211450.23222750X-RAY DIFFRACTION98
2.1544-2.21780.27031310.21862702X-RAY DIFFRACTION97
2.2178-2.28940.2481500.21772715X-RAY DIFFRACTION96
2.2894-2.37120.26791270.21772732X-RAY DIFFRACTION96
2.3712-2.46610.28851280.21262753X-RAY DIFFRACTION98
2.4661-2.57840.24191540.20722736X-RAY DIFFRACTION98
2.5784-2.71430.20641140.20112797X-RAY DIFFRACTION98
2.7143-2.88430.2531000.20212763X-RAY DIFFRACTION97
2.8843-3.10690.2311930.20682678X-RAY DIFFRACTION96
3.1069-3.41940.20761230.18712677X-RAY DIFFRACTION95
3.4194-3.91390.19921030.16422732X-RAY DIFFRACTION96
3.9139-4.92970.19731440.13962732X-RAY DIFFRACTION96
4.9297-40.790.16031650.14432643X-RAY DIFFRACTION95

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