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- PDB-6xy9: Crystal structure of haloalkane dehalogenase DbeA-M1 loop variant... -

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Basic information

Entry
Database: PDB / ID: 6xy9
TitleCrystal structure of haloalkane dehalogenase DbeA-M1 loop variant from Bradyrhizobium elkanii
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Haloalakane dehalogenase / microbial hydrolase / loop-helix engineering
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / membrane
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
ACETATE ION / Haloalkane dehalogenase
Similarity search - Component
Biological speciesBradyrhizobium elkanii USDA 94 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPrudnikova, T. / Rezacova, P. / Kuta Smatanova, I. / Chaloupkova, R. / Damborsky, J.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LQ1605 Czech Republic
Ministry of Education (MoE, Czech Republic)LM2018121 Czech Republic
Ministry of Education (MoE, Czech Republic)LM2015047 Czech Republic
Marie Sklodowska-Curie Actions, FragNET ITN792772
CitationJournal: Comput Struct Biotechnol J / Year: 2020
Title: Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family.
Authors: Marek, M. / Chaloupkova, R. / Prudnikova, T. / Sato, Y. / Rezacova, P. / Nagata, Y. / Kuta Smatanova, I. / Damborsky, J.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 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 / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
B: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7228
Polymers67,4622
Non-polymers2606
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-61 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.750, 75.130, 77.600
Angle α, β, γ (deg.)90.000, 91.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-768-

HOH

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33731.242 Da / Num. of mol.: 2 / Mutation: 143VAEEQDHAE
Source method: isolated from a genetically manipulated source
Details: artifitially synthesized
Source: (gene. exp.) Bradyrhizobium elkanii USDA 94 (bacteria)
Gene: dbeA, dhaA / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: E2RV62, haloalkane dehalogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.89 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 4000, 130 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.918 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jan 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→19.6 Å / Num. obs: 38810 / % possible obs: 98.6 % / Redundancy: 3.74 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.86 / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.76
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 6037 / CC1/2: 0.628

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k2a

4k2a


Resolution: 2.2→19.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.459 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.196 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 1938 5 %RANDOM
Rwork0.1749 ---
obs0.1779 36818 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.2 Å2 / Biso mean: 31.675 Å2 / Biso min: 12.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0 Å2-1.04 Å2
2--1.93 Å20 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 2.2→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 12 352 5011
Biso mean--32.01 33.99 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194816
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9446550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91722.591220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74115726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.411541
X-RAY DIFFRACTIONr_chiral_restr0.1280.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213739
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 140 -
Rwork0.239 2664 -
all-2804 -
obs--97.53 %

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