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- PDB-1mj5: LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT2... -

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Basic information

Entry
Database: PDB / ID: 1mj5
TitleLINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution
Components1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase
KeywordsHYDROLASE / LINB / Haloalkane dehalogenase / 1 / 3 / 4 / 6-tetrachloro-1 / 4-cyclohexadiene dehalogenase / gamma-Hexachlorocyclohexane degradation / alpha/beta-hydrolase / ultra high resolution
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / periplasmic space
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / 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 / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsOakley, A.J. / Damborsky, J. / Wilce, M.C.
Citation
Journal: Biochemistry / Year: 2004
Title: Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues.
Authors: Oakley, A.J. / Klvana, M. / Otyepka, M. / Nagata, Y. / Wilce, M.C. / Damborsky, J.
#1: Journal: Biochemistry / Year: 2002
Title: Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition
Authors: Oakley, A.J. / Prokop, Z. / Bohac, M. / Kmunicek, J. / Jedlicka, T. / Monincova, M. / Kuta-Smatanova, I. / Nagata, Y. / Damborsky, J. / Wilce, M.C.J.
#2: Journal: Biochemistry / Year: 2000
Title: Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26
Authors: Marek, J. / Vevodova, J. / Smatanova, I.K. / Nagata, Y. / Svensson, L.A. / Newman, J. / Takagi, M. / Damborsky, J.
History
DepositionAug 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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: 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1176
Polymers33,9731
Non-polymers1445
Water11,854658
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.390, 68.380, 80.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase / Haloalkane dehalogenase / 1 / 4- TCDN chlorohydrolase


Mass: 33973.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Strain: UT26 / Gene: LINB / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P51698, UniProt: D4Z2G1*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM MgCl2, 100 mM Tris HCl pH 8.5, 20% (w/v) PEG 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1200 mM1reservoirMgCl2
2100 mMTris-HCl1reservoirpH8.5
320 %(w/v)PEG40001reservoir
412 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.95→22.763 Å / Num. all: 305643 / Num. obs: 134890 / % possible obs: 83.4 % / Observed criterion σ(I): -2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.5
Reflection shellResolution: 0.95→0.97 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / % possible all: 79.7
Reflection
*PLUS
Highest resolution: 0.95 Å / Lowest resolution: 50 Å / Num. obs: 134922 / Num. measured all: 305643
Reflection shell
*PLUS
% possible obs: 79.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CV2

1cv2


Resolution: 0.95→22.763 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1411 6763 random
Rwork0.1116 --
all0.1116 134890 -
obs0.1116 134890 -
Refinement stepCycle: LAST / Resolution: 0.95→22.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 5 658 5802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.106
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_zero_chiral_vol0.115
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.95 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.994
X-RAY DIFFRACTIONs_improper_angle_d0.014
LS refinement shell
*PLUS
Highest resolution: 0.95 Å / Lowest resolution: 0.97 Å / Rfactor Rfree: 0.1202 / Rfactor Rwork: 0.0912

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