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- PDB-3dk5: Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3dk5
TitleCrystal Structure of Apo-GlmU from Mycobacterium tuberculosis
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / ACETYLTRANSFERASE / BIFUNCTIONAL / PYROPHOSPHORYLASE / ROSSMANN-LIKE FOLD / LEFT-HANDED-BETA-HELIX / TRIMER / Cell shape / Cell wall biogenesis/degradation / Cytoplasm / Magnesium / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Peptidoglycan synthesis
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / 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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsVerma, S.K. / Prakash, B.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: PknB-mediated phosphorylation of a novel substrate, N-acetylglucosamine-1-phosphate uridyltransferase, modulates its acetyltransferase activity.
Authors: Parikh, A. / Verma, S.K. / Khan, S. / Prakash, B. / Nandicoori, V.K.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6863
Polymers51,6381
Non-polymers492
Water1,838102
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)155,0599
Polymers154,9133
Non-polymers1466
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11880 Å2
ΔGint-55 kcal/mol
Surface area50690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.600, 79.600, 278.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-558-

HOH

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Components

#1: Protein Bifunctional protein glmU / UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / ...UDP-N-acetylglucosamine pyrophosphorylase / N-acetylglucosamine-1-phosphate uridyltransferase / Glucosamine-1-phosphate N-acetyltransferase


Mass: 51637.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Ra / Gene: glmU, MRA_1026 / Plasmid: pQEII / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: A5U161, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 8000, 150mM NaCl, 2mM MnCl2, 5%Glycerol, 1,3-butanediol, AMPPNP, MgCl2, DTT, pH 7.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.23→30 Å / Num. obs: 31336 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.935 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.3
Reflection shellResolution: 2.23→2.29 Å / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 10305 / Num. unique obs: 1920 / % possible all: 80.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.3 Å
Translation2.5 Å29.3 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→29.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.772 / SU B: 7.784 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1567 5 %RANDOM
Rwork0.225 ---
obs0.227 31334 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.94 Å2 / Biso mean: 43.241 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.89 Å20 Å2
2--1.78 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.23→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 2 102 3248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0213187
X-RAY DIFFRACTIONr_angle_refined_deg2.261.9554363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2055436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84123.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9981521
X-RAY DIFFRACTIONr_chiral_restr0.1570.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022384
X-RAY DIFFRACTIONr_nbd_refined0.2320.21256
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.212
X-RAY DIFFRACTIONr_mcbond_it1.5341.52263
X-RAY DIFFRACTIONr_mcangle_it2.42523485
X-RAY DIFFRACTIONr_scbond_it4.09131055
X-RAY DIFFRACTIONr_scangle_it6.1194.5878
LS refinement shellResolution: 2.233→2.291 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 95 -
Rwork0.331 1800 -
all-1895 -
obs--100 %

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