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- PDB-5h00: The crystal structure of D-2-haloacid dehalogenase -

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Basic information

Entry
Database: PDB / ID: 5h00
TitleThe crystal structure of D-2-haloacid dehalogenase
Components(R)-2-haloacid dehalogenase
KeywordsHYDROLASE / Dehalogenation / D-2-haloacid dehalogenase
Function / homology(R)-2-haloacid dehalogenase / (R)-2-haloacid dehalogenase activity / 2-haloacid dehalogenase, DehI / Halocarboxylic acid dehydrogenase DehI / AhpD-like / (R)-2-haloacid dehalogenase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWang, Y. / Xue, S.
CitationJournal: To Be Published
Title: The crystal structure of D-2-haloacid dehalogenase
Authors: Wang, Y. / Xue, S.
History
DepositionOct 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: (R)-2-haloacid dehalogenase
B: (R)-2-haloacid dehalogenase
C: (R)-2-haloacid dehalogenase
D: (R)-2-haloacid dehalogenase


Theoretical massNumber of molelcules
Total (without water)136,0594
Polymers136,0594
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-28 kcal/mol
Surface area42810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.715, 109.396, 138.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
(R)-2-haloacid dehalogenase / D-2-haloacid dehalogenase / D-DEX


Mass: 34014.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: hadD / Production host: Escherichia coli (E. coli) / References: UniProt: Q52086, (R)-2-haloacid dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MES, PEG 20000, PEG 8000, potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.64→45.24 Å / Num. obs: 42453 / % possible obs: 97.8 % / Redundancy: 8.4 % / Net I/σ(I): 9.73

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20002000data scaling
PHENIX1.9_1692model building
Coot0.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJX

3bjx


Resolution: 2.64→45.24 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.251 2126 5.01 %
Rwork0.1925 --
obs0.1955 42401 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.64→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9218 0 0 343 9561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019458
X-RAY DIFFRACTIONf_angle_d1.16912847
X-RAY DIFFRACTIONf_dihedral_angle_d14.2763464
X-RAY DIFFRACTIONf_chiral_restr0.0521379
X-RAY DIFFRACTIONf_plane_restr0.0071678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6419-2.70340.30871350.22562476X-RAY DIFFRACTION92
2.7034-2.7710.27081240.22322718X-RAY DIFFRACTION99
2.771-2.84590.31561430.22582677X-RAY DIFFRACTION99
2.8459-2.92960.31421360.22932694X-RAY DIFFRACTION99
2.9296-3.02420.29641450.22252690X-RAY DIFFRACTION99
3.0242-3.13220.3121320.23512722X-RAY DIFFRACTION99
3.1322-3.25760.31121540.22642656X-RAY DIFFRACTION99
3.2576-3.40580.26861410.21412719X-RAY DIFFRACTION99
3.4058-3.58530.27031330.19812722X-RAY DIFFRACTION99
3.5853-3.80980.22931540.18652688X-RAY DIFFRACTION99
3.8098-4.10380.23971550.18582697X-RAY DIFFRACTION99
4.1038-4.51650.23541350.16752729X-RAY DIFFRACTION99
4.5165-5.16920.22911620.16762718X-RAY DIFFRACTION98
5.1692-6.50960.231470.18862702X-RAY DIFFRACTION96
6.5096-45.24530.17251300.15082667X-RAY DIFFRACTION90

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