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- PDB-1edd: CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF H... -

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Basic information

Entry
Database: PDB / ID: 1edd
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
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
DepositionMay 13, 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 7, 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)35,2112
Polymers35,1761
Non-polymers351
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.400, 72.500, 41.300
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE DEHALOGENASE HAS BEEN SOAKED IN 10 MM SODIUM CHLORIDE. THE CHLORIDE ION WAS FOUND IN THE ACTIVE ...THE DEHALOGENASE HAS BEEN SOAKED IN 10 MM SODIUM CHLORIDE. THE CHLORIDE ION WAS FOUND IN THE ACTIVE SITE CAVITY 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 200.611-612 / PH range low: 7.2 / PH range high: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
260-70 %satammonium sulfate1drop
460-70 %satammonium sulfate1reservoir
1protein solution1drop0.005ml
3bis-Tris-H2SO41drop
5bis-Tris-H2SO41reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
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: 0.0611

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.19→15 Å / σ(F): 3 /
RfactorNum. reflection
obs0.181 12376
Refinement stepCycle: LAST / Resolution: 2.19→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 1 172 2652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg3.4
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
Highest resolution: 2.19 Å / Lowest resolution: 15 Å / Num. reflection obs: 12376 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.3 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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