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- PDB-7bkf: Crystal structure of WT BA3943, a CE4 family pseudoenzyme from Ba... -

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Basic information

Entry
Database: PDB / ID: 7bkf
TitleCrystal structure of WT BA3943, a CE4 family pseudoenzyme from Bacillus Anthracis
ComponentsPutative polysaccharide deacetylase
KeywordsUNKNOWN FUNCTION / Polysaccharide / Deacetylase / Peptidoglycan / Pseudoenzyme / Sporulation.
Function / homologySporulation protein, polysaccharide deacetylase, YlxY / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / Putative polysaccharide deacetylase
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.139 Å
AuthorsMolfetas, A. / Kokkinidis, M.
Funding support Greece, 1items
OrganizationGrant numberCountry
European Union (EU)316223 Greece
CitationJournal: To Be Published
Title: The resurrection of a dead enzyme
Authors: Molfetas, A. / Tomatsidou, N. / Bouriotis, V. / Kokkinidis, M.
History
DepositionJan 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Putative polysaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4176
Polymers32,9111
Non-polymers5065
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-57 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.441, 58.614, 78.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative polysaccharide deacetylase / Uncharacterized protein ylxY / WT BA3943


Mass: 32910.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: ylxY, BA_3943, A9486_19545, BASH2_01993, COL95_11150 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6H3AKM9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: (NH4)2SO4 CH3COONA PH=5 / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 6, 2017
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.139→40.7 Å / Num. obs: 92525 / % possible obs: 96.1 % / Redundancy: 6.0872 % / Biso Wilson estimate: 19.3 Å2 / Rrim(I) all: 0.075 / Net I/σ(I): 11.14
Reflection shellResolution: 1.14→1.21 Å / Mean I/σ(I) obs: 0.33 / Num. unique obs: 12163 / CC1/2: 0.16 / % possible all: 79

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HPA

6hpa


Resolution: 1.139→40.656 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 2100 2.27 %
Rwork0.1673 90401 -
obs0.1682 92501 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.78 Å2 / Biso mean: 24.2257 Å2 / Biso min: 12.28 Å2
Refinement stepCycle: final / Resolution: 1.139→40.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 28 249 2579
Biso mean--44.8 42.56 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042435
X-RAY DIFFRACTIONf_angle_d0.7193302
X-RAY DIFFRACTIONf_chiral_restr0.071351
X-RAY DIFFRACTIONf_plane_restr0.005424
X-RAY DIFFRACTIONf_dihedral_angle_d12.964937
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1392-1.16570.4541020.4181438371
1.1657-1.19480.47811210.4041520183
1.1948-1.22710.40031290.3616558590
1.2271-1.26320.371390.3308597497
1.2632-1.3040.30521450.27356215100
1.304-1.35060.26721440.24096223100
1.3506-1.40470.3021440.21416217100
1.4047-1.46860.25031450.19736230100
1.4686-1.54610.19741450.15796251100
1.5461-1.64290.18581460.14326259100
1.6429-1.76980.2091450.14186267100
1.7698-1.94790.16551460.1386297100
1.9479-2.22970.19071470.13616309100
2.2297-2.80910.17251480.15576386100
2.8091-40.6560.18751540.1526604100

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