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- PDB-6s42: The double mutant(Ile44Leu+Gln102His) of haloalkane dehalogenase ... -

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Basic information

Entry
Database: PDB / ID: 6s42
TitleThe double mutant(Ile44Leu+Gln102His) of haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 with an eliminated halide-binding site
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Haloalkane dehalogenase / halide-binding site / double mutant / random microseeding
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
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
HEXANE-1,6-DIOL / IODIDE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesBradyrhizobium elkanii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPudnikova, T. / Mesters, J.R. / Kuta Smatanova, I.
Funding support Czech Republic, Germany, 4items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic17-24321S Czech Republic
German Federal Ministry for Education and ResearchDAAD-16-19 Germany
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic
European Regional Development FundLM2015055 Czech Republic
CitationJournal: Crystals / Year: 2019
Title: Crystallization and Crystallographic Analysis of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site
Authors: Prudnikova, T. / Kuta Smatanova, I.
History
DepositionJun 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)35,23213
Polymers33,9931
Non-polymers1,24012
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, PISA and an analysis of crystal contacts between molecules in the unit cell and crystal packing
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-21 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.945, 63.950, 46.053
Angle α, β, γ (deg.)90.00, 106.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-411-

CL

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33992.676 Da / Num. of mol.: 1 / Mutation: Ile44Leu+Gln102His
Source method: isolated from a genetically manipulated source
Details: Chain A / Source: (gene. exp.) Bradyrhizobium elkanii (bacteria) / Gene: dbeA, dhaA / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2RV62, haloalkane dehalogenase
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, MgCl2, Tris-HCl 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→41.96 Å / Num. obs: 68322 / % possible obs: 96.13 % / Redundancy: 2.18 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.72
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.19 / Num. unique obs: 4609 / CC1/2: 0.922 / % possible all: 92.17

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k2a

4k2a


Resolution: 1.4→41.96 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 13.17
RfactorNum. reflection% reflectionSelection details
Rfree0.1522 3417 5 %0.1522
Rwork0.1398 ---
obs0.1404 68322 96.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.42 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 19 469 2730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062414
X-RAY DIFFRACTIONf_angle_d0.8733293
X-RAY DIFFRACTIONf_dihedral_angle_d8.9871352
X-RAY DIFFRACTIONf_chiral_restr0.08353
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41770.2071340.13152540X-RAY DIFFRACTION90
1.4177-1.43880.21131400.13152652X-RAY DIFFRACTION94
1.4388-1.46130.18131390.13152656X-RAY DIFFRACTION96
1.4613-1.48530.16661410.13152672X-RAY DIFFRACTION95
1.4853-1.51090.1551400.13152653X-RAY DIFFRACTION96
1.5109-1.53840.13631410.13152689X-RAY DIFFRACTION95
1.5384-1.56790.15491410.13152670X-RAY DIFFRACTION96
1.5679-1.59990.1431420.13152692X-RAY DIFFRACTION95
1.5999-1.63470.15421420.12972716X-RAY DIFFRACTION96
1.6347-1.67280.15641420.13152682X-RAY DIFFRACTION96
1.6728-1.71460.14121400.1312675X-RAY DIFFRACTION96
1.7146-1.7610.13931430.12962712X-RAY DIFFRACTION97
1.761-1.81280.15281420.13152690X-RAY DIFFRACTION97
1.8128-1.87130.16261430.13152713X-RAY DIFFRACTION97
1.8713-1.93820.15551440.13152738X-RAY DIFFRACTION97
1.9382-2.01580.16671430.13152718X-RAY DIFFRACTION97
2.0158-2.10750.16011430.13152726X-RAY DIFFRACTION97
2.1075-2.21860.14511440.13152727X-RAY DIFFRACTION97
2.2186-2.35760.13191440.13152742X-RAY DIFFRACTION98
2.3576-2.53960.16231450.13152756X-RAY DIFFRACTION97
2.5396-2.79510.17691450.13152751X-RAY DIFFRACTION97
2.7951-3.19950.14431440.13152734X-RAY DIFFRACTION97
3.1995-4.03050.13151450.13082770X-RAY DIFFRACTION97
4.0305-4.198020.15331500.13152831X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.89040.2958-0.3771.5137-0.010.7337-0.0001-0.31230.02620.2410.00930.0647-0.0204-0.19730.02380.07540.02220.02340.1439-0.02310.04-29.292.064523.8297
20.9183-0.47870.05610.6521-0.4220.4173-0.1151-0.05890.11930.09310.1044-0.058-0.138-0.0099-0.04560.09380.0186-0.00520.0977-0.02090.0846-22.72948.877815.3399
31.42660.17080.72511.68860.52550.8910.00180.0284-0.1256-0.22320.0315-0.02870.0314-0.04220.03390.0653-0.01860.01850.059-0.00750.0474-30.3737-8.41485.4932
40.9640.23430.38411.3649-0.17660.6985-0.04630.04390.0182-0.05160.0088-0.2606-0.04650.0761-0.03120.04920.00290.01340.0765-0.01060.109-14.52024.698911.6554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 298 )

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