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- PDB-7oml: Bacillus subtilis phosphoglucomutase GlmM (metal bound) -

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Basic information

Entry
Database: PDB / ID: 7oml
TitleBacillus subtilis phosphoglucomutase GlmM (metal bound)
ComponentsPhosphoglucosamine mutase
KeywordsISOMERASE / Phosphoglucosamine Mutase / glucosamine-6-phosphate / glucosamine-1-phosphate / c-di-AMP / diadenylate cyclase / metal-bound protein.
Function / homology
Function and homology information


phosphoglucosamine mutase / phosphoglucosamine mutase activity / phosphomannomutase activity / UDP-N-acetylglucosamine biosynthetic process / peptidoglycan biosynthetic process / carbohydrate metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Phosphoglucosamine mutase, bacterial type / : / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. ...Phosphoglucosamine mutase, bacterial type / : / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglucosamine mutase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPathania, M. / Grundling, A.G. / Freemont, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)P63775 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM.
Authors: Pathania, M. / Tosi, T. / Millership, C. / Hoshiga, F. / Morgan, R.M.L. / Freemont, P.S. / Grundling, A.
History
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglucosamine mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3392
Polymers50,3151
Non-polymers241
Water362
1
A: Phosphoglucosamine mutase
hetero molecules

A: Phosphoglucosamine mutase
hetero molecules


  • defined by author&software
  • Evidence: SAXS, The SAXS data of GlmM protein shows an estimate molecular weight of 83 kDa which is an indication of dimer formation., gel filtration, the protein elutes at a column length volume ...Evidence: SAXS, The SAXS data of GlmM protein shows an estimate molecular weight of 83 kDa which is an indication of dimer formation., gel filtration, the protein elutes at a column length volume that corresponds to a dimer formation.
  • 101 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)100,6784
Polymers100,6302
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2600 Å2
ΔGint-35 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.418, 134.418, 69.012
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Phosphoglucosamine mutase


Mass: 50314.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: glmM, ybbT, BSU01770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34824, phosphoglucosamine mutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.6 Å3/Da / Density % sol: 65.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 30% v/v Polyethylene glycol monomethyl ether 550 buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.9→48.15 Å / Num. obs: 15955 / % possible obs: 98.8 % / Redundancy: 20.2 % / CC1/2: 0.99 / Rpim(I) all: 0.092 / Net I/σ(I): 12.6
Reflection shellResolution: 2.9→3.08 Å / Num. unique obs: 2503 / CC1/2: 0.39 / Rpim(I) all: 1.46 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Bacillus anthracis GlmM 3PDK

3pdk


Resolution: 2.9→48.149 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 750 4.81 %
Rwork0.19 14835 -
obs0.1921 15585 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.77 Å2 / Biso mean: 45.0009 Å2 / Biso min: 13.98 Å2
Refinement stepCycle: final / Resolution: 2.9→48.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 1 2 3371
Biso mean--34.04 41.96 -
Num. residues----445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9002-3.12410.36771250.3069265787
3.1241-3.43840.28221610.2447294697
3.4384-3.93570.2541650.1851298999
3.9357-4.95780.19981520.1551307699
4.9578-48.10.17781470.1583316799

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