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- PDB-6hpa: Crystal structure of a BA3943 mutant,a CE4 family pseudoenzyme -

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Basic information

Entry
Database: PDB / ID: 6hpa
TitleCrystal structure of a BA3943 mutant,a CE4 family pseudoenzyme
ComponentsPutative polysaccharide deacetylase
KeywordsUNKNOWN FUNCTION / Polysaccharide / Deacetylase / Peptidoglycan / Pseudoenzyme / Sporulation.
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / membrane
Similarity search - Function
Sporulation protein, polysaccharide deacetylase, YlxY / : / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
Polysaccharide deacetylase / Polysaccharide deacetylase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å
AuthorsMolfetas, A. / Tomatsidou, N. / Kokkinidis, M.
Funding support Greece, 1items
OrganizationGrant numberCountry
European Union316223 Greece
CitationJournal: To Be Published
Title: The resurrection of a dean enzyme
Authors: Molfetas, A. / Tomatsidou, A. / Bouriotis, V. / Kokkinidis, M.
History
DepositionSep 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 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)32,0404
Polymers31,7251
Non-polymers3143
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, All the CE4 family of enzymes, have a predicted NodB catalytic domain.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-24 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.210, 58.816, 78.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative polysaccharide deacetylase


Mass: 31725.432 Da / Num. of mol.: 1 / Mutation: N94D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: ylxY, BA_3943, A9486_19545, BASH2_01993, CN272_11110, COL95_11150
Plasmid: pET26B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q4M7R6, UniProt: A0A6L7H2K2*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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.: 253 / 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: 2.09 Å3/Da / Density % sol: 41.19 % / Description: Cubic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Ammonium Sulphate 2.8 M Tris Buffer PH=8

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Data collection

DiffractionMean temperature: 124 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07271 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07271 Å / Relative weight: 1
ReflectionResolution: 1.554→78.883 Å / Num. obs: 38119 / % possible obs: 97.6 % / Redundancy: 12.538 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.032 / Rrim(I) all: 0.114 / Χ2: 1.33 / Net I/av σ(I): 2.85 / Net I/σ(I): 8
Reflection shellResolution: 1.554→1.559 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4864 / CC1/2: 0.798

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BC1960

Resolution: 1.554→39.441 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 1781 4.68 %
Rwork0.1646 --
obs0.1662 38043 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.554→39.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 18 253 2498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052329
X-RAY DIFFRACTIONf_angle_d0.7793154
X-RAY DIFFRACTIONf_dihedral_angle_d10.9661433
X-RAY DIFFRACTIONf_chiral_restr0.051340
X-RAY DIFFRACTIONf_plane_restr0.005404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5538-1.59580.32291420.26862797X-RAY DIFFRACTION100
1.5958-1.64280.28471530.24132829X-RAY DIFFRACTION100
1.6428-1.69580.22011540.21032801X-RAY DIFFRACTION100
1.6958-1.75640.21571260.18492817X-RAY DIFFRACTION100
1.7564-1.82680.23041560.17282809X-RAY DIFFRACTION100
1.8268-1.90990.23481390.17342630X-RAY DIFFRACTION99
1.9099-2.01060.18031180.16442457X-RAY DIFFRACTION97
2.0106-2.13650.21781340.16062843X-RAY DIFFRACTION100
2.1365-2.30150.21551140.16152533X-RAY DIFFRACTION88
2.3015-2.53310.21571060.1712904X-RAY DIFFRACTION100
2.5331-2.89950.21811420.16732887X-RAY DIFFRACTION100
2.8995-3.65270.17821490.15592913X-RAY DIFFRACTION100
3.6527-39.45420.16671480.14533042X-RAY DIFFRACTION100

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