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- PDB-1b6g: HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING CHLORIDE -

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Basic information

Entry
Database: PDB / ID: 1b6g
TitleHALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING CHLORIDE
ComponentsHALOALKANE DEHALOGENASE
KeywordsHYDROLASE / HALOALKANE DEHALOGENASE / ALPHA/BETA-HYDROLASE
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsRidder, I.S. / Rozeboom, H.J. / Dijkstra, B.W.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 A resolution.
Authors: Ridder, I.S. / Rozeboom, H.J. / Dijkstra, B.W.
#1: Journal: Biochemistry / Year: 1998
Title: Kinetic Analysis and X-Ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site
Authors: Krooshof, G.H. / Ridder, I.S. / Tepper, A.W. / Vos, G.J. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. / Janssen, D.B.
#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: 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.
#4: 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.
#5: 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
DepositionJan 14, 1999Processing site: BNL
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / struct_conn

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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)36,38611
Polymers35,5741
Non-polymers81210
Water10,827601
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.180, 72.029, 40.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2499-

HOH

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Components

#1: Protein HALOALKANE DEHALOGENASE


Mass: 35574.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Production host: Escherichia coli (E. coli) / References: UniProt: P22643, haloalkane dehalogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.5 mg/mlprotein1drop
224-26 %ammonium sulfate1dropsaturated at 273K
3100 mMMES1drop
449-53 %ammonium sulfate1reservoir
5100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9475
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 6, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 1.152→30 Å / Num. obs: 94837 / % possible obs: 97.6 % / Redundancy: 3.67 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 30.8
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.7 / % possible all: 92.5
Reflection
*PLUS
Num. measured all: 347849
Reflection shell
*PLUS
% possible obs: 92.5 %

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BE0

1be0


Resolution: 1.15→15 Å / Num. parameters: 29678 / Num. restraintsaints: 36636 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED RWORK (NO CUTOFF) FROM 16.4% TO 13.4% AND RFREE FROM 19.6% TO 17.3%. THE FOLLOWING ARE APPARENT CLOSE CONTACTS BUT ACTUALLY INVOLVE DIFFERENT ALTERNATE ...Details: ANISOTROPIC REFINEMENT REDUCED RWORK (NO CUTOFF) FROM 16.4% TO 13.4% AND RFREE FROM 19.6% TO 17.3%. THE FOLLOWING ARE APPARENT CLOSE CONTACTS BUT ACTUALLY INVOLVE DIFFERENT ALTERNATE CONFORMATIONS: CLOSE CONTACT C3 GOL 1204 - O HOH 2608 0.604 CLOSE CONTACT CD AGLU 280 - O HOH 2586 0.938 CLOSE CONTACT CE BLYS 192 - O HOH 2549 0.662 CLOSE CONTACT NH1BARG 300 - O HOH 2607 1.006 CLOSE CONTACT NZ BLYS 192 - O HOH 2549 0.874 CLOSE CONTACT O HOH 2558 - O HOH 2565 1.168 CLOSE CONTACT O HOH 2565 - O HOH 2558 1.168 CLOSE CONTACT OD1BASP 137 - O HOH 2585 0.681 CLOSE CONTACT OD2BASP 137 - O HOH 2584 0.868 CLOSE CONTACT OE1AGLU 280 - O HOH 2586 0.955 CLOSE CONTACT OE1BGLU 72 - O HOH 2591 1.117 CLOSE CONTACTCL CL 1999 - O HOH 2000 0.267
RfactorNum. reflection% reflectionSelection details
Rfree0.1454 5193 5.5 %RANDOM
all0.1051 94752 --
obs0.1059 -97.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 34 / Occupancy sum hydrogen: 2406.8 / Occupancy sum non hydrogen: 3064.8
Refinement stepCycle: LAST / Resolution: 1.15→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 49 601 3130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.121
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.08

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