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- PDB-6fv4: The structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D... -

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Basic information

Entry
Database: PDB / ID: 6fv4
TitleThe structure of N-acetyl-D-glucosamine-6-phosphate deacetylase D267A mutant from Mycobacterium smegmatis in complex with N-acetyl-D-glucosamine-6-phosphate
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-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine metabolic process / carbohydrate metabolic process / metal ion binding
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Chem-16G / : / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.974 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 CouncilBB/M017982/1 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
DepositionMar 1, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.mon_nstd_flag ..._atom_site.occupancy / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: N-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,65212
Polymers82,5452
Non-polymers1,10710
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-140 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.766, 54.437, 110.262
Angle α, β, γ (deg.)90.00, 123.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-402-

CD

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Components

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Protein / Sugars , 2 types, 3 molecules AB

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


Mass: 41272.738 Da / Num. of mol.: 2 / Mutation: D267A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: nagA, MSMEG_2119 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0QU89, N-acetylglucosamine-6-phosphate deacetylase
#3: Sugar ChemComp-16G / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE / N-acetyl-6-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-D-glucose / 2-acetamido-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-GlcpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 536 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion
Details: NagA crystals grew within a week at 295.15 K in 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 ...Details: NagA crystals grew within a week at 295.15 K in 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. 5 mM GlcNAc6P was added and incubated at 277.14 K for 30 min before crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 1.974→80.141 Å / Num. obs: 55882 / % possible obs: 96.8 % / Redundancy: 6.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.061 / Rrim(I) all: 0.152 / Net I/av σ(I): 8.5 / Net I/σ(I): 9.1
Reflection shellResolution: 1.974→2.08 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8181 / CC1/2: 0.841 / Rpim(I) all: 0.412 / Rrim(I) all: 0.987 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FV3

6fv3


Resolution: 1.974→54.56 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 2801 5.03 %
Rwork0.184 --
obs0.1865 55697 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.974→54.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5503 0 35 527 6065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075636
X-RAY DIFFRACTIONf_angle_d0.9017701
X-RAY DIFFRACTIONf_dihedral_angle_d2.7854493
X-RAY DIFFRACTIONf_chiral_restr0.055942
X-RAY DIFFRACTIONf_plane_restr0.0061018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9737-2.00780.3211360.2562638X-RAY DIFFRACTION97
2.0078-2.04430.30961440.24052667X-RAY DIFFRACTION98
2.0443-2.08360.32371530.26832592X-RAY DIFFRACTION95
2.0836-2.12610.27571450.22472651X-RAY DIFFRACTION98
2.1261-2.17230.25531520.22122679X-RAY DIFFRACTION98
2.1723-2.22290.28431270.21482676X-RAY DIFFRACTION98
2.2229-2.27850.2951950.22281736X-RAY DIFFRACTION63
2.2785-2.34010.25961230.20482684X-RAY DIFFRACTION99
2.3401-2.40890.21551450.20142714X-RAY DIFFRACTION98
2.4089-2.48670.23911410.20032668X-RAY DIFFRACTION99
2.4867-2.57560.26221520.20442702X-RAY DIFFRACTION99
2.5756-2.67870.25721730.19822674X-RAY DIFFRACTION99
2.6787-2.80060.3071500.19642708X-RAY DIFFRACTION99
2.8006-2.94820.25991520.20062703X-RAY DIFFRACTION99
2.9482-3.13290.24981440.20052740X-RAY DIFFRACTION99
3.1329-3.37480.22531230.1942758X-RAY DIFFRACTION99
3.3748-3.71430.20971250.17442501X-RAY DIFFRACTION90
3.7143-4.25160.18721310.15812749X-RAY DIFFRACTION99
4.2516-5.35590.21441640.14962776X-RAY DIFFRACTION100
5.3559-54.58110.19411260.14972880X-RAY DIFFRACTION99

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