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- PDB-2qkx: N-acetyl glucosamine 1-phosphate uridyltransferase from Mycobacte... -

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Basic information

Entry
Database: PDB / ID: 2qkx
TitleN-acetyl glucosamine 1-phosphate uridyltransferase from Mycobacterium tuberculosis complex with N-acetyl glucosamine 1-phosphate
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / rossmann / beta-helix / substrate complex / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


adhesion of symbiont to host cell / uridylyltransferase activity / 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 ...adhesion of symbiont to host cell / uridylyltransferase activity / 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 ...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
Chem-GN1 / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhang, Z. / Squire, C.J. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
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
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0632
Polymers40,7621
Non-polymers3011
Water70339
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)123,1896
Polymers122,2853
Non-polymers9043
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
Unit cell
Length a, b, c (Å)94.303, 94.303, 288.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer generated by the 3-fold axis: -x+y,-x,z and -y,x-y,z.

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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: 40761.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: glmU, Rv1018c, MT1046 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96382, UniProt: P9WMN3*PLUS, glucosamine-1-phosphate N-acetyltransferase
#2: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Lithium nitrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 30, 2007 / Details: osmic
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→42.33 Å / Num. all: 13239 / Num. obs: 13239 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 13.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 3 / Num. unique all: 1892 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HM9
Resolution: 2.75→40.42 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 26.785 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.847 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25071 651 4.9 %RANDOM
Rwork0.19514 ---
all0.19791 12588 --
obs0.19791 12588 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.32 Å20 Å2
2---0.65 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 19 39 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212852
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9713907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02824.078103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71615421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3221518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022119
X-RAY DIFFRACTIONr_nbd_refined0.2380.21227
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.28
X-RAY DIFFRACTIONr_mcbond_it0.6311.51940
X-RAY DIFFRACTIONr_mcangle_it1.1423081
X-RAY DIFFRACTIONr_scbond_it1.6113971
X-RAY DIFFRACTIONr_scangle_it2.5994.5826
LS refinement shellResolution: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 43 -
Rwork0.275 910 -
obs-43 100 %
Refinement TLS params.Method: refined / Origin x: 29.8397 Å / Origin y: -14.4516 Å / Origin z: 14.9037 Å
111213212223313233
T-0.0096 Å20.0212 Å20.0351 Å2-0.0153 Å20.0171 Å2--0.1409 Å2
L0.8554 °2-0.0067 °2-0.3531 °2-1.4863 °20.6775 °2--2.3796 °2
S0.0715 Å °-0.2161 Å °0.2638 Å °0.2726 Å °-0.0629 Å °0.178 Å °-0.3672 Å °-0.2825 Å °-0.0086 Å °

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