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- PDB-5b12: Crystal structure of the B-type halohydrin hydrogen-halide-lyase ... -

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Basic information

Entry
Database: PDB / ID: 5b12
TitleCrystal structure of the B-type halohydrin hydrogen-halide-lyase mutant F71W/Q125T/D199H from Corynebacterium sp. N-1074
ComponentsHalohydrin epoxidase B
KeywordsLYASE / Enantioselectivity / Halohydrin
Function / homology
Function and homology information


organic substance metabolic process / oxidoreductase activity / metal ion binding
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Halohydrin epoxidase B
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.721 Å
AuthorsWatanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Odaka, M. / Yohda, M.
CitationJournal: J.Biosci.Bioeng. / Year: 2016
Title: Improvement of enantioselectivity of the B-type halohydrin hydrogen-halide-lyase from Corynebacterium sp. N-1074
Authors: Watanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Odaka, M. / Yohda, M.
History
DepositionNov 17, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Feb 15, 2017Group: Other
Revision 1.3Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Halohydrin epoxidase B
B: Halohydrin epoxidase B
C: Halohydrin epoxidase B
D: Halohydrin epoxidase B
E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,36412
Polymers152,1516
Non-polymers2136
Water27,4551524
1
A: Halohydrin epoxidase B
B: Halohydrin epoxidase B
C: Halohydrin epoxidase B
D: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5768
Polymers101,4344
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint-123 kcal/mol
Surface area27860 Å2
MethodPISA
2
E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules

E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5768
Polymers101,4344
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area14330 Å2
ΔGint-119 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.913, 215.005, 104.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21E-579-

HOH

31F-520-

HOH

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Components

#1: Protein
Halohydrin epoxidase B


Mass: 25358.500 Da / Num. of mol.: 6 / Fragment: UNP residues 11-235 / Mutation: F71W, Q125T, D199H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: hheB / Plasmid: pSTT206 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q46347
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1524 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG400, ammonium sulfate, 2-propanol, PEPES

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 143723 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rsym value: 0.09 / Net I/σ(I): 37.4
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 11.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: 000)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.721→35.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 7205 5.02 %Random selection
Rwork0.1619 ---
obs0.1635 143646 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.721→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10583 0 6 1524 12113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910878
X-RAY DIFFRACTIONf_angle_d0.96414810
X-RAY DIFFRACTIONf_dihedral_angle_d14.946360
X-RAY DIFFRACTIONf_chiral_restr0.0651636
X-RAY DIFFRACTIONf_plane_restr0.0071937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7212-1.74080.26562330.20714507X-RAY DIFFRACTION100
1.7408-1.76130.27872520.20754497X-RAY DIFFRACTION100
1.7613-1.78280.23742620.19384472X-RAY DIFFRACTION100
1.7828-1.80530.24192460.18824522X-RAY DIFFRACTION100
1.8053-1.82910.22182180.19414500X-RAY DIFFRACTION100
1.8291-1.85410.25272300.1994563X-RAY DIFFRACTION100
1.8541-1.88060.23892260.19814532X-RAY DIFFRACTION100
1.8806-1.90870.26112520.194506X-RAY DIFFRACTION100
1.9087-1.93850.22852370.18574515X-RAY DIFFRACTION100
1.9385-1.97030.25232300.19034564X-RAY DIFFRACTION100
1.9703-2.00430.24612480.19084515X-RAY DIFFRACTION100
2.0043-2.04070.22832270.18354522X-RAY DIFFRACTION100
2.0407-2.07990.2282140.17734591X-RAY DIFFRACTION100
2.0799-2.12240.21882450.17654517X-RAY DIFFRACTION100
2.1224-2.16850.1952470.1694513X-RAY DIFFRACTION100
2.1685-2.2190.21932390.16484553X-RAY DIFFRACTION100
2.219-2.27450.18572400.16684535X-RAY DIFFRACTION100
2.2745-2.33590.20282440.16614549X-RAY DIFFRACTION100
2.3359-2.40470.2151990.16824561X-RAY DIFFRACTION100
2.4047-2.48230.21442480.16324591X-RAY DIFFRACTION100
2.4823-2.5710.20192510.1674539X-RAY DIFFRACTION100
2.571-2.67390.21092320.16934558X-RAY DIFFRACTION100
2.6739-2.79550.19022390.16724561X-RAY DIFFRACTION100
2.7955-2.94280.18482740.15854553X-RAY DIFFRACTION100
2.9428-3.12710.17782410.1584563X-RAY DIFFRACTION100
3.1271-3.36840.18662300.15814608X-RAY DIFFRACTION100
3.3684-3.7070.17372420.14924597X-RAY DIFFRACTION100
3.707-4.24260.16142350.12884632X-RAY DIFFRACTION100
4.2426-5.34220.13672690.12894627X-RAY DIFFRACTION100
5.3422-35.13750.16962550.15094578X-RAY DIFFRACTION95

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