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- PDB-1qh9: ENZYME-PRODUCT COMPLEX OF L-2-HALOACID DEHALOGENASE -

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Basic information

Entry
Database: PDB / ID: 1qh9
TitleENZYME-PRODUCT COMPLEX OF L-2-HALOACID DEHALOGENASE
Components2-HALOACID DEHALOGENASE(S)-2-haloacid dehalogenase
KeywordsHYDROLASE / DEHALOGENASE / ENZYME-PRODUCT COMPLEX
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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / 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
LACTIC ACID / (S)-2-haloacid dehalogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsLi, Y.-F. / Hata, Y. / Fujii, T. / Kurihara, T. / Esaki, N.
Citation
Journal: To be Published
Title: The Structure of L-2-Haloacid Dehalogenase Complexed with a Reaction Product Reveals the Mechanism of Intermediate Hydrolysis in Dehalogenase
Authors: Li, Y.-F. / Hata, Y. / Fujii, T. / Kurihara, T. / Esaki, N.
#1: 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.
History
DepositionMay 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2982
Polymers26,2081
Non-polymers901
Water28816
1
A: 2-HALOACID DEHALOGENASE
hetero molecules

A: 2-HALOACID DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5954
Polymers52,4152
Non-polymers1802
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 area17230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.810, 62.760, 51.380
Angle α, β, γ (deg.)90.00, 123.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-HALOACID DEHALOGENASE / (S)-2-haloacid dehalogenase


Mass: 26207.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH D-LACTATE / Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: YL / Gene: DEX YL / Plasmid: PKK223-3 / Gene (production host): DEX YL / Production host: Escherichia coli (E. coli) / References: UniProt: Q53464, (S)-2-haloacid dehalogenase
#2: Chemical ChemComp-LAC / LACTIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 47.7 %
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→48.63 Å / Num. obs: 8320 / % possible obs: 95.2 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.0798 / Net I/σ(I): 9.3
Reflection shellResolution: 2.5→2.8 Å / % possible all: 93.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.287 -10 %RANDOM
Rwork0.194 ---
obs-7553 91 %-
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 6 16 1763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.08
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
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.356 --
Rwork0.289 740 -
obs--79.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARA.DLATOPO.DLA
X-RAY DIFFRACTION3PARA.WATERTOPO.WATER

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