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- PDB-5lka: Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+... -

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Basic information

Entry
Database: PDB / ID: 5lka
TitleCrystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26 at 1.3 A resolution
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / haloalkane dehalogenase / bacterial enzyme / mutant
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
THIOCYANATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesSphingobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.298 Å
AuthorsDegtjarik, O. / Rezacova, P. / Iermak, I. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I.
CitationJournal: Acs Catalysis / Year: 2016
Title: Engineering a de novo transport tunnel.
Authors: Brezovsky, J. / Babkova, P. / Degtjarik, O. / Fortova, A. / Gora, A. / Iermak, I. / Rezacova, P. / Dvorak, P. / Kuta Smatanova, I. / Prokop, Z. / Chaloupkova, R. / Damborsky, J.
History
DepositionJul 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,8242
Polymers33,7661
Non-polymers581
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-5 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.867, 68.362, 80.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33766.184 Da / Num. of mol.: 1 / Mutation: W140A, F143L, L177W, I211L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium japonicum (bacteria) / Gene: linB, dhaA, SJA_C1-19590 / Production host: Escherichia coli (E. coli) / References: UniProt: D4Z2G1, haloalkane dehalogenase
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 1.91 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate, 20 % (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.298→46.87 Å / Num. obs: 64480 / % possible obs: 99.6 % / Redundancy: 6.35 % / Biso Wilson estimate: 14.49 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 16.45
Reflection shellResolution: 1.298→1.38 Å / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.5 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.4 Å40.52 Å
Translation6.4 Å40.52 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WDR

4wdr


Resolution: 1.298→40.522 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.13
RfactorNum. reflection% reflection
Rfree0.1745 2101 3.26 %
Rwork0.1385 --
obs0.1396 64467 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.72 Å2 / Biso mean: 12.6853 Å2 / Biso min: 4.03 Å2
Refinement stepCycle: final / Resolution: 1.298→40.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 3 453 2829
Biso mean--11.95 23.4 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062623
X-RAY DIFFRACTIONf_angle_d0.9213595
X-RAY DIFFRACTIONf_chiral_restr0.085370
X-RAY DIFFRACTIONf_plane_restr0.006487
X-RAY DIFFRACTIONf_dihedral_angle_d21.922992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2981-1.32830.22661340.20473975410997
1.3283-1.36150.26141390.189141154254100
1.3615-1.39830.22621380.179141054243100
1.3983-1.43950.24051380.165541044242100
1.4395-1.48590.18651400.141741464286100
1.4859-1.5390.16681390.129841114250100
1.539-1.60070.17461390.127241284267100
1.6007-1.67350.17911400.1241734313100
1.6735-1.76170.15921390.122441434282100
1.7617-1.87210.15531400.123541424282100
1.8721-2.01670.18111400.127241734313100
2.0167-2.21960.19261410.131341734314100
2.2196-2.54070.16541420.139642074349100
2.5407-3.20090.15031430.147142484391100
3.2009-40.54130.15481490.130744234572100

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