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- PDB-3d98: Crystal structure of GlmU from Mycobacterium tuberculosis, ligand... -

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Basic information

Entry
Database: PDB / ID: 3d98
TitleCrystal structure of GlmU from Mycobacterium tuberculosis, ligand-free form
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / GlmU / Uridyltransferase / acetyltransferase / Acyltransferase / Cell shape / Cell wall biogenesis/degradation / 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 morphogenesis / cell wall organization / 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
Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein glmU


Theoretical massNumber of molelcules
Total (without water)51,6381
Polymers51,6381
Non-polymers00
Water1,00956
1
A: Bifunctional protein glmU

A: Bifunctional protein glmU

A: Bifunctional protein glmU


Theoretical massNumber of molelcules
Total (without water)154,9133
Polymers154,9133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6320 Å2
ΔGint-25.4 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.270, 94.270, 284.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium formate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.85 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 2.5→42.22 Å / Num. obs: 16733 / % possible obs: 100 % / Observed criterion σ(I): 2.2 / Biso Wilson estimate: 37.13 Å2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2481 / % possible all: 100

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Processing

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

1hm9


Resolution: 2.5→42.22 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 24.37 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 803 5.08 %Random
Rwork0.1969 ---
all0.1994 15798 --
obs0.1994 15798 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 47.431 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4488 Å2-0 Å20 Å2
2---2.4488 Å2-0 Å2
3---4.8975 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 0 56 2854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072852
X-RAY DIFFRACTIONf_angle_d1.0763905
X-RAY DIFFRACTIONf_dihedral_angle_d15.765981
X-RAY DIFFRACTIONf_chiral_restr0.065493
X-RAY DIFFRACTIONf_plane_restr0.004508
LS refinement shellResolution: 2.5→2.66 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2909 135 -
Rwork0.2225 2333 -
obs--87 %

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