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- PDB-2eda: CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF H... -

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Basic information

Entry
Database: PDB / ID: 2eda
TitleCRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE
ComponentsHALOALKANE DEHALOGENASE
KeywordsDEHALOGENASE
Function / homology
Function and homology information


1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / epoxide hydrolase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.19 Å
AuthorsVerschueren, K.H.G. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1993
Title: Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site.
Authors: Verschueren, K.H. / Kingma, J. / Rozeboom, H.J. / Kalk, K.H. / Janssen, D.B. / Dijkstra, B.W.
#1: Journal: Embo J. / Year: 1991
Title: Crystal Structure of Haloalkane Dehalogenase: An Enzyme to Detoxify Halogenated Alkanes
Authors: Franken, S.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of Haloalkane Dehalogenase from Xanthobacter Autotrophicus Gj10
Authors: Rozeboom, H.J. / Kingma, J. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionAug 30, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3032
Polymers35,1761
Non-polymers1271
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.100, 73.000, 41.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUES 57 AND 168 ARE CIS PROLINES.

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Components

#1: Protein HALOALKANE DEHALOGENASE


Mass: 35175.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / References: UniProt: P22643, haloalkane dehalogenase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE DEHALOGENASE HAS BEEN SOAKED IN 5 MM IODOACETAMIDE. ONLY THE IODIDE WAS FOUND, INCLUDED BETWEEN ...THE DEHALOGENASE HAS BEEN SOAKED IN 5 MM IODOACETAMIDE. ONLY THE IODIDE WAS FOUND, INCLUDED BETWEEN TRP 125 AND TRP 175.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.74 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.2 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160-70 %satammonium sulfate1drop
260-70 %satammonium sulfate1reservoir
3protein1drop
4bis-Tris-H2SO41drop
5bis-Tris-H2SO41reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.19 Å / Lowest resolution: 9999 Å / Num. obs: 12376 / % possible obs: 81.2 % / Num. measured all: 34777 / Rmerge(I) obs: 0.061

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.19→15 Å / σ(F): 3 /
RfactorNum. reflection
obs0.161 12376
Refinement stepCycle: LAST / Resolution: 2.19→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 1 214 2694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg3.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.3 Å2

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