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- PDB-4l1g: Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine... -

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Basic information

Entry
Database: PDB / ID: 4l1g
TitleCrystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase from Bacillus cereus
ComponentsPeptidoglycan N-acetylglucosamine deacetylase
KeywordsHYDROLASE / tim barrel / polysaccharide deacetylase
Function / homology
Function and homology information


peptidoglycan-N-acetylglucosamine deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Peptidoglycan-N-acetylglucosamine deacetylase BC_1960
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.336 Å
AuthorsTsalafouta, A. / Fadouloglou, V.E. / Kokkinidis, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2017
Title: Unusual alpha-Carbon Hydroxylation of Proline Promotes Active-Site Maturation.
Authors: Fadouloglou, V.E. / Balomenou, S. / Aivaliotis, M. / Kotsifaki, D. / Arnaouteli, S. / Tomatsidou, A. / Efstathiou, G. / Kountourakis, N. / Miliara, S. / Griniezaki, M. / Tsalafouta, A. / ...Authors: Fadouloglou, V.E. / Balomenou, S. / Aivaliotis, M. / Kotsifaki, D. / Arnaouteli, S. / Tomatsidou, A. / Efstathiou, G. / Kountourakis, N. / Miliara, S. / Griniezaki, M. / Tsalafouta, A. / Pergantis, S.A. / Boneca, I.G. / Glykos, N.M. / Bouriotis, V. / Kokkinidis, M.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan N-acetylglucosamine deacetylase
B: Peptidoglycan N-acetylglucosamine deacetylase
C: Peptidoglycan N-acetylglucosamine deacetylase
D: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,60614
Polymers125,7934
Non-polymers81310
Water13,854769
1
A: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6033
Polymers31,4481
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6033
Polymers31,4481
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6994
Polymers31,4481
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6994
Polymers31,4481
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.657, 92.657, 242.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Peptidoglycan N-acetylglucosamine deacetylase


Mass: 31448.307 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: bc1960, BC_1960 / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q81EK9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 769 / 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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.817 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2009 / Details: monochromators
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.817 Å / Relative weight: 1
ReflectionResolution: 2.336→80 Å / Num. obs: 45861 / % possible obs: 100 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1
Reflection shellResolution: 2.336→2.3868 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W1B

1w1b


Resolution: 2.336→30.639 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2282 5.04 %RANDOM
Rwork0.1792 ---
obs0.1814 45341 98.86 %-
all-45310 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.336→30.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6842 0 46 769 7657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037099
X-RAY DIFFRACTIONf_angle_d0.7589632
X-RAY DIFFRACTIONf_dihedral_angle_d10.7762578
X-RAY DIFFRACTIONf_chiral_restr0.0551039
X-RAY DIFFRACTIONf_plane_restr0.0041238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.336-2.38680.29111180.23922409X-RAY DIFFRACTION90
2.3868-2.44230.24341490.21962623X-RAY DIFFRACTION99
2.4423-2.50340.30931350.2142687X-RAY DIFFRACTION99
2.5034-2.5710.28721410.20952642X-RAY DIFFRACTION99
2.571-2.64660.29131470.20232652X-RAY DIFFRACTION100
2.6466-2.7320.26471400.2132679X-RAY DIFFRACTION100
2.732-2.82960.25271440.20172656X-RAY DIFFRACTION100
2.8296-2.94280.24991370.19842649X-RAY DIFFRACTION100
2.9428-3.07660.24281600.19342690X-RAY DIFFRACTION99
3.0766-3.23860.25321400.18892679X-RAY DIFFRACTION99
3.2386-3.44130.22361510.17822720X-RAY DIFFRACTION100
3.4413-3.70660.20041310.16162723X-RAY DIFFRACTION100
3.7066-4.07880.19981350.1582716X-RAY DIFFRACTION99
4.0788-4.66730.1791550.13782762X-RAY DIFFRACTION100
4.6673-5.87350.18251500.16112791X-RAY DIFFRACTION100
5.8735-30.64170.21461490.19262950X-RAY DIFFRACTION99

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