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- PDB-5gzx: The complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA -

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Basic information

Entry
Database: PDB / ID: 5gzx
TitleThe complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA
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-Chloropropionic acid / (R)-2-haloacid dehalogenase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWang, Y. / Xue, S.
CitationJournal: To Be Published
Title: The complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7748
Polymers140,3404
Non-polymers4344
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-28 kcal/mol
Surface area43020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.300, 95.687, 108.813
Angle α, β, γ (deg.)90.00, 108.03, 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: 35084.996 Da / Num. of mol.: 4 / Mutation: D205N
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: Chemical
ChemComp-RCI / (R)-2-Chloropropionic acid / (R)-2-Chloropropanoic acid


Mass: 108.524 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5ClO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: PEG 20000, PEG 8000, MES, potassium sodium tartrate tetrahydrate, BaCl2

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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: 2.35→49.32 Å / Num. obs: 57707 / % possible obs: 98 % / Redundancy: 6.9 % / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
HKL-20002000data scaling
PHENIX1.9-1692phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJX

3bjx


Resolution: 2.35→49.32 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 29.06
RfactorNum. reflection% reflection
Rfree0.2559 2903 5.04 %
Rwork0.2007 --
obs0.2034 57707 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9308 0 24 376 9708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089572
X-RAY DIFFRACTIONf_angle_d1.09113000
X-RAY DIFFRACTIONf_dihedral_angle_d14.0963500
X-RAY DIFFRACTIONf_chiral_restr0.0421396
X-RAY DIFFRACTIONf_plane_restr0.0061700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3491-2.38760.26691330.23942415X-RAY DIFFRACTION93
2.3876-2.42880.30981510.23342583X-RAY DIFFRACTION98
2.4288-2.47290.2991370.2292600X-RAY DIFFRACTION98
2.4729-2.52050.27531460.21722589X-RAY DIFFRACTION98
2.5205-2.57190.30621390.22612607X-RAY DIFFRACTION98
2.5719-2.62790.25241310.21722613X-RAY DIFFRACTION98
2.6279-2.6890.31621340.21742601X-RAY DIFFRACTION98
2.689-2.75620.25981290.20782634X-RAY DIFFRACTION98
2.7562-2.83070.28451310.20842531X-RAY DIFFRACTION97
2.8307-2.9140.25971430.21612632X-RAY DIFFRACTION99
2.914-3.00810.31831320.21452641X-RAY DIFFRACTION99
3.0081-3.11560.24961330.22162594X-RAY DIFFRACTION98
3.1156-3.24030.27391310.21372649X-RAY DIFFRACTION99
3.2403-3.38770.26031540.20862619X-RAY DIFFRACTION99
3.3877-3.56630.27371280.19422636X-RAY DIFFRACTION99
3.5663-3.78960.2391510.18612585X-RAY DIFFRACTION97
3.7896-4.08210.2341350.1872634X-RAY DIFFRACTION99
4.0821-4.49270.24271390.18052658X-RAY DIFFRACTION99
4.4927-5.14220.23971530.18352633X-RAY DIFFRACTION99
5.1422-6.47630.25211400.20982641X-RAY DIFFRACTION98
6.4763-49.32950.19781330.17452639X-RAY DIFFRACTION96

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