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- PDB-5o6y: Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine... -

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Basic information

Entry
Database: PDB / ID: 5o6y
TitleCrystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide
Components(Peptidoglycan N-acetylglucosamine ...) x 2
KeywordsHYDROLASE / inhibitor / complex / deacetylase / peptidoglycan
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
4-naphthalen-1-yl-~{N}-oxidanyl-benzamide / Chem-PE3 / DI(HYDROXYETHYL)ETHER / Peptidoglycan-N-acetylglucosamine deacetylase BC_1960
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsFadouloglou, V.E. / Kotsifaki, D. / Kokkinidis, M.
Funding support1items
OrganizationGrant numberCountry
European UnionInnovCrete
Citation
Journal: To Be Published
Title: Crystal structure of the Bc1960 peptidoglycan N-acetylglucosamine deacetylase in complex with 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide
Authors: Fadouloglou, V.E. / Kotsifaki, D. / Kokkinidis, M.
#1: Journal: 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 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)102,51162
Polymers96,9944
Non-polymers5,51758
Water13,475748
1
A: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,05818
Polymers24,2361
Non-polymers1,82117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,43020
Polymers24,2521
Non-polymers1,17719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,90414
Polymers24,2521
Non-polymers1,65213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,11910
Polymers24,2521
Non-polymers8679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.042, 93.042, 243.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Peptidoglycan N-acetylglucosamine ... , 2 types, 4 molecules ABCD

#1: Protein Peptidoglycan N-acetylglucosamine deacetylase


Mass: 24236.398 Da / Num. of mol.: 1
Mutation: Post-translational modification P171PXU in the chains B, C and D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Gene: BC_1960 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q81EK9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein Peptidoglycan N-acetylglucosamine deacetylase


Mass: 24252.398 Da / Num. of mol.: 3 / Mutation: post-translational midification of P171 to PXU
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Gene: BC_1960 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q81EK9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 10 types, 806 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-5YA / 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide


Mass: 263.291 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H13NO2
#5: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H58O15
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#8: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 4000 16-20%, ammonium sulfate 0.2M, sodium acetate buffer 0.1 M
PH range: 4.2-5.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 2.5→48.77 Å / Num. obs: 38009 / % possible obs: 99.4 % / Redundancy: 11.4 % / CC1/2: 0.971 / Rmerge(I) obs: 0.555 / Rpim(I) all: 0.169 / Rrim(I) all: 0.581 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 9.7 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.61.3640.8230.4511.4495.3
9.01-48.770.10.9650.0340.10699.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L1G

4l1g


Resolution: 2.498→46.521 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1886 4.99 %
Rwork0.1957 --
obs0.1988 37800 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.498→46.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6815 0 249 748 7812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027207
X-RAY DIFFRACTIONf_angle_d0.5249758
X-RAY DIFFRACTIONf_dihedral_angle_d19.7972586
X-RAY DIFFRACTIONf_chiral_restr0.0421034
X-RAY DIFFRACTIONf_plane_restr0.0041235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4977-2.56520.32891190.25232481X-RAY DIFFRACTION91
2.5652-2.64070.29791400.22712737X-RAY DIFFRACTION100
2.6407-2.72590.30491640.22092693X-RAY DIFFRACTION100
2.7259-2.82330.25911220.21532761X-RAY DIFFRACTION100
2.8233-2.93640.28111350.21652744X-RAY DIFFRACTION100
2.9364-3.070.25761330.19882750X-RAY DIFFRACTION100
3.07-3.23180.27831490.19922759X-RAY DIFFRACTION100
3.2318-3.43420.2461600.1822736X-RAY DIFFRACTION100
3.4342-3.69930.23641680.17212770X-RAY DIFFRACTION100
3.6993-4.07140.22831630.16072779X-RAY DIFFRACTION100
4.0714-4.660.19021590.14482801X-RAY DIFFRACTION100
4.66-5.86930.21921520.1732847X-RAY DIFFRACTION100
5.8693-46.5290.24161220.23613056X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 35.7506 Å / Origin y: -2.7786 Å / Origin z: -30.5155 Å
111213212223313233
T0.1209 Å20.0327 Å20.0616 Å2-0.0048 Å2-0.0372 Å2---0.0245 Å2
L0.02 °2-0.0031 °2-0.0145 °2-0.0602 °20.0443 °2--0.0425 °2
S-0.0384 Å °0.0117 Å °-0.0118 Å °0.0419 Å °0.0596 Å °0.0303 Å °0.0351 Å °0.0367 Å °0.0139 Å °
Refinement TLS groupSelection details: all

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