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- PDB-5gzy: The complex structure of D-2-haloacid dehalogenase with L-LA -

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Basic information

Entry
Database: PDB / ID: 5gzy
TitleThe complex structure of D-2-haloacid dehalogenase with L-LA
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 / (2S)-2-HYDROXYPROPANOIC ACID / (R)-2-haloacid dehalogenase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWang, Y. / Xue, S.
CitationJournal: To Be Published
Title: The complex structure of D-2-haloacid dehalogenase with L-LA
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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4208
Polymers136,0594
Non-polymers3604
Water27,0951504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-26 kcal/mol
Surface area42560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.945, 95.136, 109.058
Angle α, β, γ (deg.)90.00, 98.09, 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: 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: Chemical
ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1504 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MES, PEG 20000, PEG 8000, potassium sodium tartrate tetrahydrate, D-2-chloropropionate

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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: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.18→47.57 Å / Num. obs: 76730 / % possible obs: 99.4 % / Redundancy: 6.7 % / Net I/σ(I): 9.78

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20002000data scaling
PHENIX1.9_1692data processing
Coot0.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJX

3bjx


Resolution: 2.18→47.57 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.03
RfactorNum. reflection% reflection
Rfree0.1969 3847 5.01 %
Rwork0.1578 --
obs0.1598 76721 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 0 24 1504 10832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089566
X-RAY DIFFRACTIONf_angle_d1.0312992
X-RAY DIFFRACTIONf_dihedral_angle_d13.2463500
X-RAY DIFFRACTIONf_chiral_restr0.041398
X-RAY DIFFRACTIONf_plane_restr0.0061698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1787-2.20630.27991220.18492313X-RAY DIFFRACTION86
2.2063-2.23530.2391220.18342706X-RAY DIFFRACTION100
2.2353-2.26590.24861500.17562739X-RAY DIFFRACTION100
2.2659-2.29830.24391420.17162663X-RAY DIFFRACTION100
2.2983-2.33260.21221540.16982688X-RAY DIFFRACTION100
2.3326-2.3690.181440.16622730X-RAY DIFFRACTION100
2.369-2.40790.22761320.16732694X-RAY DIFFRACTION100
2.4079-2.44940.21321420.17292745X-RAY DIFFRACTION100
2.4494-2.49390.24571260.18452716X-RAY DIFFRACTION100
2.4939-2.54190.22351470.16772696X-RAY DIFFRACTION100
2.5419-2.59380.23541430.16842685X-RAY DIFFRACTION100
2.5938-2.65020.23051440.16722688X-RAY DIFFRACTION100
2.6502-2.71180.20321640.16072712X-RAY DIFFRACTION100
2.7118-2.77960.20341330.1642710X-RAY DIFFRACTION100
2.7796-2.85480.19651360.16762705X-RAY DIFFRACTION100
2.8548-2.93880.21151480.16312699X-RAY DIFFRACTION100
2.9388-3.03360.19711520.16612717X-RAY DIFFRACTION100
3.0336-3.1420.19711480.16242701X-RAY DIFFRACTION100
3.142-3.26780.19811300.15962708X-RAY DIFFRACTION100
3.2678-3.41650.18651330.15152731X-RAY DIFFRACTION100
3.4165-3.59650.18961450.14382738X-RAY DIFFRACTION100
3.5965-3.82180.16641510.13662707X-RAY DIFFRACTION100
3.8218-4.11670.18961340.14822725X-RAY DIFFRACTION100
4.1167-4.53070.15521690.13312730X-RAY DIFFRACTION100
4.5307-5.18560.1631490.14222721X-RAY DIFFRACTION100
5.1856-6.53070.19591340.16772746X-RAY DIFFRACTION100
6.5307-47.57930.16551530.14562761X-RAY DIFFRACTION99

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