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- PDB-6fv3: Crystal structure of N-acetyl-D-glucosamine-6-phosphate deacetyla... -

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Basic information

Entry
Database: PDB / ID: 6fv3
TitleCrystal structure of N-acetyl-D-glucosamine-6-phosphate deacetylase from Mycobacterium smegmatis.
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsHYDROLASE / N-acetyl-D-glucosamine-6-phosphate mycobacteria / carbohydrate metabolism
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / metal ion binding
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsAhangar, M.S. / Furze, C.M. / Guy, C.S. / Cooper, C. / Maskew, K.S. / Graham, B. / Cameron, A.D. / Fullam, E.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
Wellcome Trust201442/Z/16/A United Kingdom
Wellcome Trust and Royal society104193/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M01116X/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBM017982/1 United Kingdom
Royal SocietyRG120405 United Kingdom
Wellcome Trust105627/Z/14/Z United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional determination of homologs of theMycobacterium tuberculosis N-acetylglucosamine-6-phosphate deacetylase (NagA).
Authors: Ahangar, M.S. / Furze, C.M. / Guy, C.S. / Cooper, C. / Maskew, K.S. / Graham, B. / Cameron, A.D. / Fullam, E.
History
DepositionFeb 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
C: N-acetylglucosamine-6-phosphate deacetylase
D: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,79012
Polymers165,2674
Non-polymers5238
Water5,801322
1
A: N-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8956
Polymers82,6332
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-164 kcal/mol
Surface area26400 Å2
MethodPISA
2
C: N-acetylglucosamine-6-phosphate deacetylase
D: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8956
Polymers82,6332
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-164 kcal/mol
Surface area25750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.450, 86.390, 89.930
Angle α, β, γ (deg.)88.12, 75.58, 69.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
N-acetylglucosamine-6-phosphate deacetylase


Mass: 41316.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 / Gene: nagA, MSMEG_2119 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QU89, N-acetylglucosamine-6-phosphate deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion
Details: NagA crystals grew in a condition containing 0.12 M monosaccharide mix (Morpheus, Molecular Dimensions), 0.1 M imidazole/MES pH 6.5, 20 % PEG 500 MME, 10 % w/v PEG 20000 with the addition of ...Details: NagA crystals grew in a condition containing 0.12 M monosaccharide mix (Morpheus, Molecular Dimensions), 0.1 M imidazole/MES pH 6.5, 20 % PEG 500 MME, 10 % w/v PEG 20000 with the addition of 10 mM CdCl2 additive.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.58→55.23 Å / Num. obs: 51044 / % possible obs: 98.2 % / Redundancy: 2.6 % / CC1/2: 0.96 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.173 / Rrim(I) all: 0.245 / Net I/σ(I): 4.3
Reflection shellResolution: 2.58→2.6296 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 1 / Num. unique obs: 555 / CC1/2: 0.434 / Rpim(I) all: 0.902 / Rrim(I) all: 0.059 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P50

2p50


Resolution: 2.58→51.951 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.44
RfactorNum. reflection% reflection
Rfree0.2951 2494 4.89 %
Rwork0.2473 --
obs0.2496 51006 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.58→51.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10714 0 8 322 11044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510915
X-RAY DIFFRACTIONf_angle_d0.95714884
X-RAY DIFFRACTIONf_dihedral_angle_d4.5636490
X-RAY DIFFRACTIONf_chiral_restr0.0571814
X-RAY DIFFRACTIONf_plane_restr0.0051975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.62960.4121290.36972745X-RAY DIFFRACTION98
2.6296-2.68330.3821270.35082613X-RAY DIFFRACTION97
2.6833-2.74160.38361530.34392712X-RAY DIFFRACTION98
2.7416-2.80540.35641550.31632680X-RAY DIFFRACTION98
2.8054-2.87560.34911510.31872681X-RAY DIFFRACTION98
2.8756-2.95330.35141550.28892627X-RAY DIFFRACTION98
2.9533-3.04020.33241370.27632714X-RAY DIFFRACTION98
3.0402-3.13830.33691360.28232667X-RAY DIFFRACTION98
3.1383-3.25050.36821330.27572703X-RAY DIFFRACTION98
3.2505-3.38060.38771270.27532722X-RAY DIFFRACTION98
3.3806-3.53440.29281300.27152733X-RAY DIFFRACTION98
3.5344-3.72070.27541370.23642701X-RAY DIFFRACTION98
3.7207-3.95370.28591490.22782708X-RAY DIFFRACTION99
3.9537-4.25890.28061290.21512695X-RAY DIFFRACTION99
4.2589-4.68720.22251380.19162722X-RAY DIFFRACTION98
4.6872-5.36490.24751440.20372698X-RAY DIFFRACTION99
5.3649-6.75680.22741100.21542756X-RAY DIFFRACTION99
6.7568-51.96160.23121540.1952635X-RAY DIFFRACTION97

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