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- PDB-1hde: HALOALKANE DEHALOGENASE MUTANT WITH PHE 172 REPLACED WITH TRP -

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Basic information

Entry
Database: PDB / ID: 1hde
TitleHALOALKANE DEHALOGENASE MUTANT WITH PHE 172 REPLACED WITH TRP
ComponentsHALOALKANE DEHALOGENASE
KeywordsDEHALOGENASE / HYDROLASE / DETOXIFICATION
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
Haloalkane dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsRidder, I.S. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1996
Title: Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range.
Authors: Schanstra, J.P. / Ridder, I.S. / Heimeriks, G.J. / Rink, R. / Poelarends, G.J. / Kalk, K.H. / Dijkstra, B.W. / Janssen, D.B.
#1: 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.
#2: 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.
#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
DepositionAug 8, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE
B: HALOALKANE DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)70,4302
Polymers70,4302
Non-polymers00
Water0
1
A: HALOALKANE DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)35,2151
Polymers35,2151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HALOALKANE DEHALOGENASE


Theoretical massNumber of molelcules
Total (without water)35,2151
Polymers35,2151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.680, 73.530, 41.600
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.997561, -0.056672, 0.040741), (-0.056932, -0.998364, 0.005252), (0.040376, -0.007558, -0.999156)
Vector: -48.531, 12.078, 39.561)

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Components

#1: Protein HALOALKANE DEHALOGENASE /


Mass: 35214.832 Da / Num. of mol.: 2 / Mutation: F172W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Cell line: BL21 / Plasmid: PGELAF+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22643, haloalkane dehalogenase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
152-56 %(w/v)satammonium sulfate1reservoir
2100 mMMES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15796 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.101
Reflection
*PLUS
Highest resolution: 2.67 Å / Lowest resolution: 35 Å / Num. measured all: 43099
Reflection shell
*PLUS
Highest resolution: 2.67 Å / Lowest resolution: 2.77 Å / % possible obs: 83.1 % / Rmerge(I) obs: 0.312

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 2.7→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.258 -
Rwork0.205 -
obs0.205 14413
Displacement parametersBiso mean: 13.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 0 0 4964
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.9

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