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- PDB-3d8v: Crystal structure of GlmU from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 3d8v
TitleCrystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-N-acetylglucosamine
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / Nucleotide-diphospho-sugar transferases/Single-stranded left-handed beta-helix / Acyltransferase / Cell shape / Cell wall biogenesis/degradation / Cytoplasm / Magnesium / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Peptidoglycan synthesis
Function / homology
Function and homology information


uridylyltransferase activity / adhesion of symbiont to host cell / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / entry of bacterium into host cell / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process ...uridylyltransferase activity / adhesion of symbiont to host cell / glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / entry of bacterium into host cell / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhang, Z. / Squire, C.J. / Baker, E.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure and function of GlmU from Mycobacterium tuberculosis.
Authors: Zhang, Z. / Bulloch, E.M. / Bunker, R.D. / Baker, E.N. / Squire, C.J.
History
DepositionMay 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2452
Polymers51,6381
Non-polymers6071
Water2,648147
1
A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,7356
Polymers154,9133
Non-polymers1,8223
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12600 Å2
ΔGint-57.7 kcal/mol
Surface area53080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.238, 114.238, 361.796
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Bifunctional protein glmU / / [Includes: UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) (N-acetylglucosamine-1-phosphate ...[Includes: UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) (N-acetylglucosamine-1-phosphate uridyltransferase) / Glucosamine-1-phosphate N-acetyltransferase (EC 2.3.1.157)]


Mass: 51637.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glmU, Rv1018c, MT1046 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P96382, UniProt: P9WMN3*PLUS, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 4.4 Å3/Da / Density % sol: 72.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% PEG 8000, 0.1 M Cacodylate, 9% MPD, 12% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2007
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.55→42.49 Å / Num. obs: 31984 / Observed criterion σ(I): 1 / Redundancy: 11.8 % / Biso Wilson estimate: 49.01 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.3
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HM9

1hm9


Resolution: 2.55→33.979 Å / SU ML: 0.32 / Isotropic thermal model: anisotropic / Phase error: 25.27 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2439 1528 5.07 %
Rwork0.1989 --
obs0.2013 30117 99.94 %
all-31984 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.341 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--4.9017 Å2-0 Å20 Å2
2---4.9017 Å2-0 Å2
3---2.9959 Å2
Refinement stepCycle: LAST / Resolution: 2.55→33.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 39 147 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073564
X-RAY DIFFRACTIONf_angle_d1.0674884
X-RAY DIFFRACTIONf_dihedral_angle_d17.5441243
X-RAY DIFFRACTIONf_chiral_restr0.064604
X-RAY DIFFRACTIONf_plane_restr0.004636
LS refinement shellResolution: 2.55→2.63 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2743 116 -
Rwork0.2384 2575 -
obs--100 %

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