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- PDB-6f9o: Crystal structure of cold-adapted haloalkane dehalogenase DpcA fr... -

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Basic information

Entry
Database: PDB / ID: 6f9o
TitleCrystal structure of cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Microbial enzymes / haloalkane dehalogenases / HLDs / Alpha/Beta-hydrolase fold enzymes / 2 domains / the highest activity towards 1-bromobutane / 1-bromohexane and 1 / 3-dibromopropane
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / 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
DI(HYDROXYETHYL)ETHER / Haloalkane dehalogenase
Similarity search - Component
Biological speciesPsychrobacter cryohalolentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsTratsiak, K. / Prudnikova, T. / Drienovska, I. / Damborsky, J. / Brynda, J. / Pachl, P. / Kuty, M. / Chaloupkova, R. / Kuta Smatanova, I. / Rezacova, P.
Funding support Czech Republic, 9items
OrganizationGrant numberCountry
Grant AgencyGACR 17-24321S/P305 Czech Republic
Grant AgencyGA16-24223S Czech Republic
Grant AgencyGA16-06096S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO1214 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO1304 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLQ1605 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015051 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015047 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015055 Czech Republic
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5.
Authors: Tratsiak, K. / Prudnikova, T. / Drienovska, I. / Damborsky, J. / Brynda, J. / Pachl, P. / Kuty, M. / Chaloupkova, R. / Rezacova, P. / Kuta Smatanova, I.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallographic analysis of new psychrophilic haloalkane dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17.
Authors: Tratsiak, K. / Degtjarik, O. / Drienovska, I. / Chrast, L. / Rezacova, P. / Kuty, M. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I.
#2: Journal: Appl. Environ. Microbiol. / Year: 2012
Title: Biochemical characterization of a novel haloalkane dehalogenase from a cold-adapted bacterium.
Authors: Drienovska, I. / Chovancova, E. / Koudelakova, T. / Damborsky, J. / Chaloupkova, R.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 15, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5389
Polymers34,9131
Non-polymers6248
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, using the elution buffer consisting of 50 mM Tris-HCl at pH 7.5 with the presence of 150 mM NaCl. A Superdex 200 10/300 GL column (GE Healthcare, Waukesha, WI) was ...Evidence: gel filtration, using the elution buffer consisting of 50 mM Tris-HCl at pH 7.5 with the presence of 150 mM NaCl. A Superdex 200 10/300 GL column (GE Healthcare, Waukesha, WI) was calibrated with aldolase (158 kDa), conalbumin (75 kDa), ovalbumin (44 kDa), carbonic anhydratase (29 kDa), and RNase A (13,7 kDa).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-28 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.332, 79.451, 43.489
Angle α, β, γ (deg.)90.00, 94.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloalkane dehalogenase /


Mass: 34913.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gram-negative psychrophilic bacteria Psychrobacter
Source: (gene. exp.) Psychrobacter cryohalolentis (strain K5) (bacteria)
Strain: K5 / Gene: dhmA, Pcryo_1253 / Plasmid: pET21b / Details (production host): T7 promoter
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): DE3 / References: UniProt: Q1QBB9, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.04 Å3/Da / Density % sol: 39.63 % / Description: Needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.88
Details: 0.2 M ammonium acetate, 30%(w/v) PEG 4000 and 0.1 M sodium acetate trihydrate pH 4.6 and with the addition of 0.6 ul of 0.1M L-proline (Additive Screen kit, Hampton Research) to the crystallization drop
PH range: 4.6-5.9 / Temp details: 292-295

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Cryojet XTL system (Oxford Instruments)
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97826 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 1, 2012 / Details: Sagitally bended Si111 crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97826 Å / Relative weight: 1
ReflectionResolution: 1.05→20 Å / Num. obs: 120315 / % possible obs: 92.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.716 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.053 / Net I/σ(I): 39.7
Reflection shellResolution: 1.05→1.09 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 7363 / % possible all: 56.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000VERSION November 1, 2011data reduction
HKL-3000VERSION November 1, 2011data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B6G

1b6g


Resolution: 1.05→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.543 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13151 6066 5 %RANDOM
Rwork0.11033 ---
obs0.11139 114202 91.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.671 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 28 576 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192740
X-RAY DIFFRACTIONr_bond_other_d0.0020.022445
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9453748
X-RAY DIFFRACTIONr_angle_other_deg1.0335721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67124.058138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24415442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6821518
X-RAY DIFFRACTIONr_chiral_restr0.0970.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213156
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02570
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.710.6451324
X-RAY DIFFRACTIONr_mcbond_other0.710.6451323
X-RAY DIFFRACTIONr_mcangle_it1.0230.9781683
X-RAY DIFFRACTIONr_mcangle_other1.0220.9791684
X-RAY DIFFRACTIONr_scbond_it1.0830.8041416
X-RAY DIFFRACTIONr_scbond_other1.0820.8041416
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3221.1472059
X-RAY DIFFRACTIONr_long_range_B_refined2.69310.3673451
X-RAY DIFFRACTIONr_long_range_B_other2.6933452
X-RAY DIFFRACTIONr_rigid_bond_restr2.27335182
X-RAY DIFFRACTIONr_sphericity_free22.7615305
X-RAY DIFFRACTIONr_sphericity_bonded7.17855399
LS refinement shellResolution: 1.048→1.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 244 -
Rwork0.218 4716 -
obs--51.27 %

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