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- PDB-7wkq: Crystal Structure of halohydrin dehalogenase from Acidimicrobiia ... -

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Basic information

Entry
Database: PDB / ID: 7wkq
TitleCrystal Structure of halohydrin dehalogenase from Acidimicrobiia bacterium
Componentshalohydrin dehalogenase
KeywordsBIOSYNTHETIC PROTEIN / halohydrin dehalogenase
Function / homologyShort-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesAcidimicrobiia bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsWan, N.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Identification and Structure Analysis of an Unusual Halohydrin Dehalogenase for Highly Chemo-, Regio- and Enantioselective Bio-Nitration of Epoxides.
Authors: Wang, H.H. / Wan, N.W. / Miao, R.P. / He, C.L. / Chen, Y.Z. / Liu, Z.Q. / Zheng, Y.G.
History
DepositionJan 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 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: halohydrin dehalogenase
B: halohydrin dehalogenase
C: halohydrin dehalogenase
D: halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)104,7754
Polymers104,7754
Non-polymers00
Water00
1
A: halohydrin dehalogenase
B: halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)52,3872
Polymers52,3872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-24 kcal/mol
Surface area18820 Å2
MethodPISA
2
C: halohydrin dehalogenase

D: halohydrin dehalogenase


Theoretical massNumber of molelcules
Total (without water)52,3872
Polymers52,3872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area2930 Å2
ΔGint-26 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.823, 103.047, 105.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
halohydrin dehalogenase


Mass: 26193.744 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidimicrobiia bacterium (bacteria) / Gene: CK520_03170 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2G4FD71

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.89→46.33 Å / Num. obs: 41486 / % possible obs: 99.61 % / Redundancy: 9.9 % / Biso Wilson estimate: 82.61 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Net I/σ(I): 31.23
Reflection shellResolution: 2.89→3 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 4246 / Rpim(I) all: 0.3375 / % possible all: 98.79

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I9V

6i9v


Resolution: 2.89→46.33 Å / SU ML: 0.4221 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2488 3752 9.23 %
Rwork0.2192 36897 -
obs0.2219 40649 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.54 Å2
Refinement stepCycle: LAST / Resolution: 2.89→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 0 0 6560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01176664
X-RAY DIFFRACTIONf_angle_d1.63199028
X-RAY DIFFRACTIONf_chiral_restr0.10671045
X-RAY DIFFRACTIONf_plane_restr0.00921196
X-RAY DIFFRACTIONf_dihedral_angle_d26.03992374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.930.43691180.42961310X-RAY DIFFRACTION94.01
2.93-2.970.37461480.36861342X-RAY DIFFRACTION98.81
2.97-3.010.35181410.36411381X-RAY DIFFRACTION99.54
3.01-3.050.36091330.33271386X-RAY DIFFRACTION99.87
3.05-3.10.36431410.3221345X-RAY DIFFRACTION99.46
3.1-3.150.34431420.3141382X-RAY DIFFRACTION99.48
3.15-3.20.39271450.30891350X-RAY DIFFRACTION99.73
3.2-3.250.29241150.28771415X-RAY DIFFRACTION99.61
3.25-3.310.32531590.29041358X-RAY DIFFRACTION99.74
3.31-3.380.24671380.26691348X-RAY DIFFRACTION99.73
3.38-3.440.31361410.26511400X-RAY DIFFRACTION99.74
3.44-3.520.34181470.24591365X-RAY DIFFRACTION99.67
3.52-3.60.27671340.22721366X-RAY DIFFRACTION99.6
3.6-3.690.2291510.24081370X-RAY DIFFRACTION100
3.69-3.790.26181440.21211384X-RAY DIFFRACTION99.67
3.79-3.90.25891370.2281355X-RAY DIFFRACTION99.8
3.9-4.030.24471380.2071344X-RAY DIFFRACTION99.8
4.03-4.170.25841380.2151383X-RAY DIFFRACTION99.09
4.17-4.340.27061410.20041389X-RAY DIFFRACTION99.61
4.34-4.540.22331420.18921363X-RAY DIFFRACTION99.87
4.54-4.770.20481340.18291370X-RAY DIFFRACTION99.54
4.78-5.070.19441390.18211388X-RAY DIFFRACTION99.93
5.07-5.460.24061380.20871372X-RAY DIFFRACTION99.74
5.47-6.010.31811390.22731343X-RAY DIFFRACTION98.8
6.01-6.880.24061430.22521370X-RAY DIFFRACTION99.47
6.88-8.660.16961420.17881382X-RAY DIFFRACTION99.93
8.67-46.330.1781240.16461336X-RAY DIFFRACTION96.56

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