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- PDB-6hm9: Crystal structure of a BA3943 mutant,a CE4 family pseudoenzyme wi... -

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Basic information

Entry
Database: PDB / ID: 6hm9
TitleCrystal structure of a BA3943 mutant,a CE4 family pseudoenzyme with restored enzymatic activity.
ComponentsPutative polysaccharide deacetylase
KeywordsUNKNOWN FUNCTION / NodB / Polysaccharide / Deacetylation / Resurrected / Pseudoenzyme.
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process
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
ACETATE ION / Polysaccharide deacetylase / Polysaccharide deacetylase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71311 Å
AuthorsMolfetas, A. / Tomatsidou, A. / Kokkinidis, M.
Funding support Greece, 1items
OrganizationGrant numberCountry
European Union316223 Greece
CitationJournal: To Be Published
Title: The resurrection of a dead enzyme.
Authors: Molfetas, A. / Tomasidou, A. / Kokkinidis, M.
History
DepositionSep 12, 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

Downloads & links

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Assembly

Deposited unit
A: Putative polysaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9726
Polymers32,5281
Non-polymers4435
Water4,143230
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-51 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.950, 59.030, 78.500
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: 32528.246 Da / Num. of mol.: 1 / Mutation: N94D V95D A183R
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) / Strain (production host): B / BL21-DE3 [Korea] / References: UniProt: A0A1Q4M7R6, UniProt: A0A6L7H2K2*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 41.11 %
Description: Cubic crystals, grown very rapidly, usually in 2-3 hours.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Ammonium Sulphate 2.8 M, Acetate Buffer PH=5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2016
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.71311→47.1792 Å / Num. obs: 54811 / % possible obs: 99.6817 % / Redundancy: 12.755 % / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Net I/σ(I): 22.36
Reflection shellResolution: 1.71→1.76 Å / Rmerge(I) obs: 0.047 / Num. unique obs: 2064 / CC1/2: 0.999 / Rpim(I) all: 0.014 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimless0.5.17data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BC1960

Resolution: 1.71311→47.1792 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.1952 2749 5.02 %
Rwork0.1669 --
obs0.1684 54796 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71311→47.1792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 24 230 2479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062336
X-RAY DIFFRACTIONf_angle_d0.7843161
X-RAY DIFFRACTIONf_dihedral_angle_d11.3841432
X-RAY DIFFRACTIONf_chiral_restr0.052337
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7131-1.74270.28331350.25432449X-RAY DIFFRACTION94
1.7427-1.77430.25971380.20932646X-RAY DIFFRACTION100
1.7743-1.80850.25321350.19352572X-RAY DIFFRACTION100
1.8085-1.84540.27221400.17932630X-RAY DIFFRACTION100
1.8454-1.88550.21631390.18482579X-RAY DIFFRACTION100
1.8855-1.92940.20351380.17012636X-RAY DIFFRACTION100
1.9294-1.97760.20381380.16172613X-RAY DIFFRACTION100
1.9776-2.03110.17761400.15872595X-RAY DIFFRACTION100
2.0311-2.09090.20641340.17282633X-RAY DIFFRACTION100
2.0909-2.15830.19421360.1642590X-RAY DIFFRACTION100
2.1583-2.23550.25211360.1652603X-RAY DIFFRACTION100
2.2355-2.3250.17851350.16612619X-RAY DIFFRACTION100
2.325-2.43080.22511360.1742622X-RAY DIFFRACTION100
2.4308-2.5590.19621370.1782621X-RAY DIFFRACTION100
2.559-2.71930.23411330.18382598X-RAY DIFFRACTION100
2.7193-2.92920.22081370.18192624X-RAY DIFFRACTION100
2.9292-3.22390.21951380.1782587X-RAY DIFFRACTION100
3.2239-3.69030.17391430.15352622X-RAY DIFFRACTION100
3.6903-4.64870.13171390.13262607X-RAY DIFFRACTION100
4.6487-47.19710.19041420.17182601X-RAY DIFFRACTION100

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