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- PDB-7ojr: Bacillus subtilis phosphoglucomutase GlmM (phosphate bound) -

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Basic information

Entry
Database: PDB / ID: 7ojr
TitleBacillus subtilis phosphoglucomutase GlmM (phosphate bound)
ComponentsPhosphoglucosamine mutase
KeywordsISOMERASE / Phosphoglucosamine Mutase / glucosamine-6-phosphate / glucosamine-1-phosphate / c-di-AMP / diadenylate cyclase / TRANSFERASE
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-phosphohexomutase superfamily / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. ...Phosphoglucosamine mutase, bacterial type / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / 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, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / 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
Similarity search - Domain/homology
PHOSPHATE ION / Phosphoglucosamine mutase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 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 17, 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)50,4102
Polymers50,3151
Non-polymers951
Water00
1
A: Phosphoglucosamine mutase
hetero molecules

A: Phosphoglucosamine mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8204
Polymers100,6302
Non-polymers1902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2710 Å2
ΔGint-31 kcal/mol
Surface area35510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.876, 134.876, 69.180
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)
Strain: 168 / Gene: glmM, ybbT, BSU01770 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34824, phosphoglucosamine mutase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M buffer system 1 (Imidazole; MES, pH 6.5), 0.09 M NPS (NaN03; Na2HPO4; (NH4)2SO4) and 37.5% MPD_P1K_P3350 (75% MPD, PEG 1K, PEG 3350)

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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: Sep 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.05→48.29 Å / Num. obs: 14081 / % possible obs: 99.9 % / Redundancy: 19.6 % / CC1/2: 0.54 / Rpim(I) all: 0.13 / Net I/σ(I): 6.9
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2497 / Rpim(I) all: 2.58 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHASERphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PDK (B. anthracis GlmM structure)

3pdk


Resolution: 3.05→48.29 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 738 5.32 %
Rwork0.2029 13146 -
obs0.2057 13884 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.41 Å2 / Biso mean: 50.7728 Å2 / Biso min: 21.9 Å2
Refinement stepCycle: final / Resolution: 3.05→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 5 0 3373
Biso mean--65.82 --
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 (%)
3.05-3.28650.35441420.3441247294
3.2865-3.61710.26761620.2384258199
3.6171-4.14020.23311320.18662660100
4.1402-5.21530.2131680.15772664100
5.2153-48.290.25751340.17862769100
Refinement TLS params.Method: refined / Origin x: -59.4914 Å / Origin y: 18.3021 Å / Origin z: 32.7673 Å
111213212223313233
T0.4159 Å20.0593 Å2-0.0875 Å2-0.2519 Å2-0.0163 Å2--0.3195 Å2
L0.3459 °20.1185 °20.011 °2-2.0016 °20.5855 °2--0.9486 °2
S-0.0766 Å °-0.0151 Å °0.0344 Å °0.1738 Å °0.2147 Å °-0.1186 Å °0.2056 Å °0.1247 Å °-0.0915 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 446
2X-RAY DIFFRACTION1allB1

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