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- PDB-2dhe: CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKAN... -

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Basic information

Entry
Database: PDB / ID: 2dhe
TitleCRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE
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: 2.13 Å
AuthorsVerschueren, K.H.G. / Dijkstra, B.W.
Citation
Journal: Nature / Year: 1993
Title: Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase.
Authors: Verschueren, K.H. / Seljee, F. / Rozeboom, H.J. / Kalk, K.H. / 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
DepositionJun 24, 1993Processing site: BNL
Revision 1.0Aug 31, 1994Provider: 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)35,2112
Polymers35,1761
Non-polymers351
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.000, 72.600, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO 57 / 2: CIS PROLINE - PRO 168

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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.: 185 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURE SPECIFICATIONS ARE AS IN 2HAD.
Sequence detailsTHERE IS A DISCREPANCY BETWEEN THE SEQUENCE OBTAINED FROM THE SWISS-PROT ENTRY AND THE SEQUENCE ...THERE IS A DISCREPANCY BETWEEN THE SEQUENCE OBTAINED FROM THE SWISS-PROT ENTRY AND THE SEQUENCE OBTAINED FOUND IN ENTRY FOR RESIDUE 120 (ILE 120 IN THE SWISS-PROT ENTRY, LEU 120 IN THIS ENTRY). THE SWISS-PROT ENTRY IS IN ERROR AND THE DEPOSITORS HAVE REQUESTED THAT THE SEQUENCE DATABANKS MAKE THE PROPER CORRECTIONS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal grow
*PLUS
pH: 6.2 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 %(w/v)sat1reservoir(NH4)2SO4
2100 mMbis-Tris1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.14 Å / Num. all: 14119 / Num. obs: 1284 / % possible obs: 84.7 % / Num. measured all: 36467 / Rmerge(I) obs: 0.0574

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.13→15 Å / σ(F): 3 /
RfactorNum. reflection
obs0.171 14119
Refinement stepCycle: LAST / Resolution: 2.13→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 1 185 2665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg2.9
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.165 / Highest resolution: 2.14 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.9

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