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- PDB-7f2z: Crystal structure of OxdB E85A mutant (form II) -

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Basic information

Entry
Database: PDB / ID: 7f2z
TitleCrystal structure of OxdB E85A mutant (form II)
ComponentsPhenylacetaldoxime dehydratase
KeywordsLYASE / Aldoxime dehydratase / heme
Function / homologyphenylacetaldoxime dehydratase / phenylacetaldoxime dehydratase activity / Haem-containing dehydratase / Haem-containing dehydratase / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Phenylacetaldoxime dehydratase
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
B: Phenylacetaldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5754
Polymers83,3422
Non-polymers1,2332
Water1,44180
1
A: Phenylacetaldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2872
Polymers41,6711
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-21 kcal/mol
Surface area14500 Å2
MethodPISA
2
B: Phenylacetaldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2872
Polymers41,6711
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-21 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.662, 62.662, 359.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Phenylacetaldoxime dehydratase


Mass: 41670.863 Da / Num. of mol.: 2 / 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) / References: UniProt: P82604, EC: 4.99.1.7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M sodium citrate and 0.1M sodium cacodylate pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→39.919 Å / Num. obs: 37816 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 49.17 Å2 / Rmerge(I) obs: 0.07735 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.8271 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 3621 / % possible all: 98.4

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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: 2.3→39.92 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1890 5 %Random selection
Rwork0.182 ---
obs0.184 37815 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 86 80 5479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085600
X-RAY DIFFRACTIONf_angle_d0.9417673
X-RAY DIFFRACTIONf_dihedral_angle_d14.2723233
X-RAY DIFFRACTIONf_chiral_restr0.053808
X-RAY DIFFRACTIONf_plane_restr0.006982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35740.39771280.34782440X-RAY DIFFRACTION97
2.3574-2.42110.33011330.27012535X-RAY DIFFRACTION100
2.4211-2.49240.30131310.25782497X-RAY DIFFRACTION100
2.4924-2.57280.3421320.23072514X-RAY DIFFRACTION100
2.5728-2.66470.33851330.22582515X-RAY DIFFRACTION100
2.6647-2.77140.30361330.22462531X-RAY DIFFRACTION100
2.7714-2.89750.27621340.22192540X-RAY DIFFRACTION100
2.8975-3.05020.2991330.22072545X-RAY DIFFRACTION100
3.0502-3.24120.23871360.19932568X-RAY DIFFRACTION100
3.2412-3.49140.26051360.18792588X-RAY DIFFRACTION100
3.4914-3.84250.2371350.16572565X-RAY DIFFRACTION100
3.8425-4.39790.1971370.14432597X-RAY DIFFRACTION100
4.3979-5.53850.18291400.13912668X-RAY DIFFRACTION100
5.5385-39.9190.19451490.16152822X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5531-0.0321-0.18052.67740.47283.867-0.0403-0.4001-0.3109-0.00340.0769-0.02310.122-0.3336-0.00510.2208-0.0255-0.00480.32760.08430.29147.2483-22.841215.0956
22.9407-0.11180.15592.8601-0.11833.2364-0.17830.03020.0280.0174-0.01240.0754-0.324-0.07950.17780.22440.0207-0.00490.47730.01210.2902-28.4241-15.132646.9372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 1 THROUGH 339)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 1 THROUGH 339)

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