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- PDB-5h01: The crystal structure of D-2-halacid dehalogenase mutant -

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Basic information

Entry
Database: PDB / ID: 5h01
TitleThe crystal structure of D-2-halacid dehalogenase mutant
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: 2.194 Å
AuthorsXue, S. / Wang, Y.
CitationJournal: To Be Published
Title: The crystal structure of D-2-halacid dehalogenase mutant
Authors: Xue, S. / Wang, Y.
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

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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)140,3444
Polymers140,3444
Non-polymers00
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-31 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.713, 97.181, 93.750
Angle α, β, γ (deg.)90.00, 107.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35085.980 Da / Num. of mol.: 4 / Mutation: L288I
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.: 435 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 289 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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.19→48.591 Å / Num. obs: 75088 / % possible obs: 95.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 7.8
Reflection shellResolution: 2.19→2.23 Å

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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: 2.194→48.591 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3122 3776 5.04 %
Rwork0.2533 --
obs0.2562 74968 95.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→48.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9308 0 0 435 9743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099552
X-RAY DIFFRACTIONf_angle_d1.2112976
X-RAY DIFFRACTIONf_dihedral_angle_d14.8633500
X-RAY DIFFRACTIONf_chiral_restr0.0471392
X-RAY DIFFRACTIONf_plane_restr0.0071696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1942-2.2220.3731180.31322055X-RAY DIFFRACTION75
2.222-2.25120.36451120.30692194X-RAY DIFFRACTION80
2.2512-2.2820.40121240.29962309X-RAY DIFFRACTION84
2.282-2.31460.31551270.29592359X-RAY DIFFRACTION86
2.3146-2.34920.32981280.29642456X-RAY DIFFRACTION89
2.3492-2.38590.38521260.28842501X-RAY DIFFRACTION91
2.3859-2.4250.35051540.29532619X-RAY DIFFRACTION94
2.425-2.46680.38061400.28612586X-RAY DIFFRACTION96
2.4668-2.51170.30081300.2842710X-RAY DIFFRACTION97
2.5117-2.560.351540.26672665X-RAY DIFFRACTION97
2.56-2.61220.28161210.2692728X-RAY DIFFRACTION98
2.6122-2.6690.33491490.26892708X-RAY DIFFRACTION99
2.669-2.73110.34121580.26342711X-RAY DIFFRACTION99
2.7311-2.79940.31761350.25322763X-RAY DIFFRACTION99
2.7994-2.87510.32311500.26242720X-RAY DIFFRACTION99
2.8751-2.95970.29481260.27272760X-RAY DIFFRACTION99
2.9597-3.05520.34321310.2562747X-RAY DIFFRACTION100
3.0552-3.16440.31031470.27042736X-RAY DIFFRACTION99
3.1644-3.2910.34381700.25632736X-RAY DIFFRACTION100
3.291-3.44080.30661390.25272753X-RAY DIFFRACTION100
3.4408-3.62210.30681550.24962745X-RAY DIFFRACTION99
3.6221-3.8490.28591430.23272766X-RAY DIFFRACTION100
3.849-4.1460.31241400.22522752X-RAY DIFFRACTION100
4.146-4.5630.26661370.21472789X-RAY DIFFRACTION100
4.563-5.22260.2911550.21882785X-RAY DIFFRACTION100
5.2226-6.57730.29651590.24832759X-RAY DIFFRACTION99
6.5773-48.60240.26241480.23632780X-RAY DIFFRACTION97

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