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- PDB-6xt8: Crystal structure of haloalkane dehalogenase variant DhaA115 doma... -

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Basic information

Entry
Database: PDB / ID: 6xt8
TitleCrystal structure of haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
ComponentsHaloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
KeywordsHYDROLASE / Haloalkane dehalogenase
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Haloalkane dehalogenase
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMarkova, K. / Damborsky, J. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
CitationJournal: Acs Catalysis / Year: 2021
Title: Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers
Authors: Markova, K. / Kunka, A. / Chmelova, K. / Havlasek, M. / Babkova, P. / Marques, S.M. / Vasina, M. / Planas-Iglesias, J. / Chaloupkova, R. / Bednar, D. / Prokop, Z. / Damborsky, J. / Marek, M.
History
DepositionJan 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
B: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
C: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
D: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,89418
Polymers137,7904
Non-polymers1,10514
Water12,304683
1
A: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
B: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,59010
Polymers68,8952
Non-polymers6968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15800 Å2
ΔGint-125 kcal/mol
Surface area21900 Å2
MethodPISA
2
C: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
D: Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3048
Polymers68,8952
Non-polymers4096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15430 Å2
ΔGint-130 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.900, 164.613, 92.736
Angle α, β, γ (deg.)90.000, 100.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Haloalkane dehalogenase variant DhaA115 domain-swapped dimer type-2


Mass: 34447.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3G2*PLUS, haloalkane dehalogenase

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Non-polymers , 5 types, 697 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG 3350, ammonium nitrate, bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.7→47 Å / Num. obs: 141424 / % possible obs: 97.8 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Rrim(I) all: 0.053 / Net I/σ(I): 16 / Num. measured all: 652840 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.734.50.6013137969050.8070.310.6792.595.2
9.31-474.70.021429890510.010.02348.699.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZG

4hzg


Resolution: 1.7→45.528 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.88
RfactorNum. reflection% reflection
Rfree0.2147 7006 4.96 %
Rwork0.1847 --
obs0.1862 141366 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.93 Å2 / Biso mean: 28.2553 Å2 / Biso min: 12.09 Å2
Refinement stepCycle: final / Resolution: 1.7→45.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9478 0 67 693 10238
Biso mean--39.79 34.55 -
Num. residues----1164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.3172230.2898445696
1.7193-1.73950.30662320.2733444698
1.7395-1.76080.29482420.2584445198
1.7608-1.78310.31332190.2616452898
1.7831-1.80650.32282340.2611444298
1.8065-1.83130.2922440.2582437897
1.8313-1.85740.29912290.2478423192
1.8574-1.88510.28191970.2338450098
1.8851-1.91460.27592240.2256449498
1.9146-1.9460.26492450.2208456499
1.946-1.97960.24062210.2149451499
1.9796-2.01560.25732530.216448699
2.0156-2.05430.27252420.2202453399
2.0543-2.09620.25012280.2131445099
2.0962-2.14180.23872100.2108459999
2.1418-2.19170.22452300.2044447899
2.1917-2.24650.24352640.2071453999
2.2465-2.30720.24482570.1924442698
2.3072-2.37510.22662210.1916432893
2.3751-2.45170.23442200.2013440397
2.4517-2.53940.24182240.1955455099
2.5394-2.6410.2512290.1965463499
2.641-2.76120.22262290.1885451799
2.7612-2.90680.22622460.1917452199
2.9068-3.08880.21452750.1848449699
3.0888-3.32730.20672380.1725451898
3.3273-3.6620.17462180.164429493
3.662-4.19150.18652320.1496457299
4.1915-5.27960.14982290.1345457699
5.2796-45.5280.15742510.1587443696

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