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- PDB-1jud: L-2-HALOACID DEHALOGENASE -

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Basic information

Entry
Database: PDB / ID: 1jud
TitleL-2-HALOACID DEHALOGENASE
ComponentsL-2-HALOACID DEHALOGENASE
KeywordsDEHALOGENASE / HYDROLASE
Function / homology
Function and homology information


(S)-2-haloacid dehalogenase / (S)-2-haloacid dehalogenase activity
Similarity search - Function
L-2-Haloacid dehalogenase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...L-2-Haloacid dehalogenase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsHisano, T. / Hata, Y. / Fujii, T. / Liu, J.-Q. / Kurihara, T. / Esaki, N. / Soda, K.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.
Authors: Hisano, T. / Hata, Y. / Fujii, T. / Liu, J.Q. / Kurihara, T. / Esaki, N. / Soda, K.
#1: Journal: Proteins / Year: 1996
Title: Crystallization of L-2-Haloacid Dehalogenase from Pseudomonas Sp. Yl
Authors: Hisano, T. / Hata, Y. / Fujii, T. / Kurihara, T. / Esaki, N. / Soda, K.
History
DepositionJun 3, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: L-2-HALOACID DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)26,2081
Polymers26,2081
Non-polymers00
Water1,11762
1
A: L-2-HALOACID DEHALOGENASE

A: L-2-HALOACID DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)52,4152
Polymers52,4152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2970 Å2
ΔGint-21 kcal/mol
Surface area18450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.210, 62.780, 50.840
Angle α, β, γ (deg.)90.00, 122.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-2-HALOACID DEHALOGENASE


Mass: 26207.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: YL / Gene: L-DEX YL / Plasmid: PKK223-3 / Gene (production host): L-DEX YL / Production host: Escherichia coli (E. coli) / References: UniProt: Q53464, (S)-2-haloacid dehalogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlenzyme solution1drop
250 mMpotassium dihydrogenphosphate1reservoir
315 %(w/v)PEG80001reservoir
41 %(v/v)n-propanol alcohol1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 7, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→43 Å / Num. obs: 8124 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.0397
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.109 / % possible all: 90.3
Reflection
*PLUS
Num. measured all: 31020

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
R-AXISIICdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.193 --
obs0.193 7849 94.4 %
Displacement parametersBiso mean: 14.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 62 1819
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.318
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.33
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.075
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.143 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.33
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.075

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