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- PDB-1cij: HALOALKANE DEHALOGENASE SOAKED WITH HIGH CONCENTRATION OF BROMIDE -

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Basic information

Entry
Database: PDB / ID: 1cij
TitleHALOALKANE DEHALOGENASE SOAKED WITH HIGH CONCENTRATION OF BROMIDE
ComponentsPROTEIN (HALOALKANE DEHALOGENASE)
KeywordsHYDROLASE / DEHALOGENASE / COLLISION COMPLEX / ALPHA/BETA-HYDROLASE
Function / homology
Function and homology information


1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase 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
BROMIDE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsRidder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystallographic and kinetic evidence of a collision complex formed during halide import in haloalkane dehalogenase.
Authors: Pikkemaat, M.G. / Ridder, I.S. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. / Janssen, D.B.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined X-ray structures of haloalkane dehalogenase at pH 6.2 and pH 8.2 and implications for the reaction mechanism.
Authors: Verschueren, K.H. / Franken, S.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#3: 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.
#4: 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
DepositionMar 31, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Sep 29, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Nov 20, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: PROTEIN (HALOALKANE DEHALOGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4014
Polymers35,1621
Non-polymers2403
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.407, 71.964, 40.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (HALOALKANE DEHALOGENASE) / DHLA


Mass: 35161.770 Da / Num. of mol.: 1 / Mutation: I2V
Source method: isolated from a genetically manipulated source
Details: BROMIDE ION / Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Production host: Escherichia coli (E. coli) / References: UniProt: P22643, haloalkane dehalogenase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISCREPANCY AT 2 IS DUE TO EXPRESSION SYSTEM

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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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growpH: 5.8
Details: 50 % AMMONIUM SULFATE 100 MM MES BUFFER, PH 5.9 , pH 5.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5.9 / PH range high: 5.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
2100 mMMES1drop
347-53 %ammonium sulfate1reservoir
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Dec 24, 1997 / Details: DOUBLE MIRRORS (MAC-XOS)
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 12688 / % possible obs: 97.6 % / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.108 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.363 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 34688 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.363

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1BE0

1be0


Resolution: 2.3→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED
Cross valid method: THROUGHOUT, EXCEPT LAST STEP IN WHICH ALL DATA (WORK+TEST SET) WERE USED
σ(F): 0
Details: THE VALUES LISTED AS WORKING IN REMARK 3 APPLY TO THE LAST CYCLE OF THE REFINEMENT IN WHICH ALL DATA (WORK + FREE) WERE USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1000 7.8 %RANDOM EXTENSION OF SET USED FOR 1BE0 MODEL
Rwork0.226 ---
obs-11923 93.1 %-
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 3 160 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.831.5
X-RAY DIFFRACTIONx_mcangle_it4.182
X-RAY DIFFRACTIONx_scbond_it4.12
X-RAY DIFFRACTIONx_scangle_it5.552.5
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.363 125 8.8 %
Rwork0.305 1299 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.WATTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 7.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 8.8 % / Rfactor Rwork: 0.305

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