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- PDB-7f2y: Crystal structure of OxdB E85A mutant (form I) -

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Basic information

Entry
Database: PDB / ID: 7f2y
TitleCrystal structure of OxdB E85A mutant (form I)
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: 1.55 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)42,2872
Polymers41,6711
Non-polymers6161
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-20 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.306, 63.774, 59.246
Angle α, β, γ (deg.)90.00, 94.22, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 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: 0.9 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: 1.55→36.06 Å / Num. obs: 51535 / % possible obs: 99.29 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03188 / Rpim(I) all: 0.02042 / Rrim(I) all: 0.03798 / Net I/σ(I): 19.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5184 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 5040 / CC1/2: 0.733 / Rpim(I) all: 0.3276 / Rrim(I) all: 0.6151 / % possible all: 97.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Cootmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3a15

3a15


Resolution: 1.55→36.06 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.129 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19896 5167 10 %RANDOM
Rwork0.17186 ---
obs0.17455 46369 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.26 Å2
2---0.66 Å20 Å2
3---1.44 Å2
Refinement stepCycle: 1 / Resolution: 1.55→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 43 163 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132860
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172539
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6693927
X-RAY DIFFRACTIONr_angle_other_deg1.5191.5845873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0223.088136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23615442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7171510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023270
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4062.1771376
X-RAY DIFFRACTIONr_mcbond_other1.4072.1761375
X-RAY DIFFRACTIONr_mcangle_it1.9463.2691725
X-RAY DIFFRACTIONr_mcangle_other1.9453.271726
X-RAY DIFFRACTIONr_scbond_it1.9112.3521484
X-RAY DIFFRACTIONr_scbond_other1.9122.3531482
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7733.452192
X-RAY DIFFRACTIONr_long_range_B_refined4.07625.8333237
X-RAY DIFFRACTIONr_long_range_B_other4.05225.5833211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 381 -
Rwork0.304 3283 -
obs--96.93 %
Refinement TLS params.Method: refined / Origin x: 10.6736 Å / Origin y: 29.1359 Å / Origin z: 14.1156 Å
111213212223313233
T0.0337 Å2-0.0079 Å20.0072 Å2-0.0208 Å2-0.0025 Å2--0.0063 Å2
L2.0691 °2-0.1288 °20.4586 °2-1.4457 °2-0.0433 °2--1.2268 °2
S-0.0491 Å °-0.1312 Å °-0.048 Å °-0.0292 Å °0.0041 Å °0.0135 Å °0.0345 Å °-0.0315 Å °0.0451 Å °

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