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- PDB-7pw1: Crystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA -

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Basic information

Entry
Database: PDB / ID: 7pw1
TitleCrystal structure of ancestral haloalkane dehalogenase AncLinB-DmbA
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / Ancestral enzyme / BALBES
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMazur, A. / Grinkevich, P. / Prudnikova, T.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Other government17/2019/P
Other governmentCZ.02.1.01/0.0/0.0/15_003/0000441
Other governmentCZ.02.1.01/0.0/0.0/16_026/0008451 Czech Republic
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA.
Authors: Mazur, A. / Grinkevich, P. / Chaloupkova, R. / Havlickova, P. / Kascakova, B. / Kuty, M. / Damborsky, J. / Kuta Smatanova, I. / Prudnikova, T.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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

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Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5407
Polymers33,3501
Non-polymers1896
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-38 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.897, 68.897, 156.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-764-

HOH

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Components

#1: Protein Haloalkane dehalogenase


Mass: 33350.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 4000, 0.1 M sodium citrate pH 5.6, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 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: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→63.04 Å / Num. obs: 61367 / % possible obs: 99.6 % / Redundancy: 10.45 % / CC1/2: 0.99 / Net I/σ(I): 13.68
Reflection shellResolution: 1.5→1.59 Å / Mean I/σ(I) obs: 1.65 / Num. unique obs: 9534 / CC1/2: 0.77 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QVB

2qvb


Resolution: 1.5→63.04 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.495 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17395 3064 5 %RANDOM
Rwork0.1384 ---
obs0.14017 58297 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.5→63.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 9 317 2657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0460.0192509
X-RAY DIFFRACTIONr_bond_other_d0.0060.022274
X-RAY DIFFRACTIONr_angle_refined_deg2.9681.9513418
X-RAY DIFFRACTIONr_angle_other_deg1.35735268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62223.435131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10715406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6621525
X-RAY DIFFRACTIONr_chiral_restr0.2050.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212877
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02552
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_it1.4631.8681220
X-RAY DIFFRACTIONr_mcbond_other1.4591.8651219
X-RAY DIFFRACTIONr_mcangle_it1.4592.8011537
X-RAY DIFFRACTIONr_mcangle_other1.462.8031538
X-RAY DIFFRACTIONr_scbond_it2.772.1881289
X-RAY DIFFRACTIONr_scbond_other2.772.1881289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4293.1721879
X-RAY DIFFRACTIONr_long_range_B_refined2.22824.0383006
X-RAY DIFFRACTIONr_long_range_B_other2.12623.262924
X-RAY DIFFRACTIONr_rigid_bond_restr6.97934783
X-RAY DIFFRACTIONr_sphericity_free10.4995207
X-RAY DIFFRACTIONr_sphericity_bonded4.04554829
LS refinement shellResolution: 1.5→1.535 Å
RfactorNum. reflection% reflection
Rfree0.254 215 -
Rwork0.229 4064 -
obs--95.86 %

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