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

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Basic information

Entry
Database: PDB / ID: 3spt
TitleCrystal structure of GlmU from Mycobacterium tuberculosis in complex with ACETYL COENZYME A and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / ACETYLTRANSFERASE / BIFUNCTIONAL / PYROPHOSPHORYLASE / ROSSMANN-LIKE FOLD / LEFT-HANDED-BETA-HELIX / CELL SHAPE / CELL WALL BIOGENESIS/DEGRADATION / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / PEPTIDOGLYCAN SYNTHESIS / ACYLTRANSFERASE
Function / homology
Function and homology information


entry of bacterium into host cell / 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 / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process ...entry of bacterium into host cell / 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 / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / membrane / 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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 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
ACETYL COENZYME *A / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsJagtap, P.A. / Prakash, B.
CitationJournal: to be published
Title: Structure of Mycobacterium tuberculosis GlmU in complex with Acetyl CoA
Authors: Jagtap, P.A. / Verma, S.K. / Prakash, B.
History
DepositionJul 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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)53,9566
Polymers52,4671
Non-polymers1,4905
Water3,819212
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)161,86918
Polymers157,4003
Non-polymers4,47015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16780 Å2
ΔGint-175 kcal/mol
Surface area53560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.194, 110.194, 361.295
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-500-

MG

21A-617-

HOH

31A-647-

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: 52466.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: glmU, MT1046, Rv1018c / Plasmid: pQEII / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA
References: UniProt: P96382, UniProt: P9WMN3*PLUS, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 212 / 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: 4.02 Å3/Da / Density % sol: 69.43 %
Crystal growTemperature: 291 K / Method: sitting drop / pH: 8.5
Details: 0.1M Tris-Cl, pH-8.5, 2% Tacsimate, 18% PEG 3350, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARCCD 225 / Detector: CCD / Date: Jan 29, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionNumber: 268386 / Rmerge(I) obs: 0.054 / D res high: 2.33 Å / Num. obs: 36542 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
10.4219.6846797.710.023
7.3710.4279310010.024
6.027.37101610010.028
5.216.02118210010.031
4.665.21133199.910.029
4.264.66143410010.029
3.944.26159110010.033
3.693.94166910010.038
3.473.69180810010.042
3.33.47188710010.05
3.143.3197510010.062
3.013.14207510010.076
2.893.01214910010.094
2.792.89224710010.121
2.692.79230210010.151
2.612.69240310010.179
2.532.61247210010.217
2.462.53251810010.278
2.392.46258810010.314
2.332.39263598.310.359
ReflectionResolution: 2.33→19.808 Å / Num. obs: 36542 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.057 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.33-2.390.3440.3595.0518654268026350.38798.3
2.39-2.460.2730.3146.0919269258925880.338100
2.46-2.530.2440.2786.9218824251825180.298100
2.53-2.610.1760.2178.7618397247324720.234100
2.61-2.690.1570.17910.3517867240324030.193100
2.69-2.790.1210.15112.5117158230223020.163100
2.79-2.890.1010.12115.1916738224722470.13100
2.89-3.010.070.09419.3316014214921490.101100
3.01-3.140.0560.07623.1315375207520750.082100
3.14-3.30.0440.06228.1114630197519750.067100
3.3-3.470.0330.053313973188718870.054100
3.47-3.690.0270.04238.3213292180818080.046100
3.69-3.940.0240.03842.6312218166916690.041100
3.94-4.260.020.03346.8611650159115910.036100
4.26-4.660.0170.02952.3310435143414340.031100
4.66-5.210.0170.02952.69615133213310.03199.9
5.21-6.020.0170.03149.528512118211820.033100
6.02-7.370.0160.02851.297273101610160.03100
7.37-10.420.0120.02460.3855407937930.026100
10.420.0120.02358.9829524784670.02597.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DJ4

3dj4


Resolution: 2.33→19.68 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2134 / WRfactor Rwork: 0.1879 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8552 / SU B: 4.712 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1942 / SU Rfree: 0.1718 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.22359 1001 2.7 %RANDOM
Rwork0.19205 ---
obs0.19291 35443 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.66 Å2 / Biso mean: 31.524 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.0001 Å2
Refinement stepCycle: LAST / Resolution: 2.33→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 93 212 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0213619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3531.9864957
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1865473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.423.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.171531
X-RAY DIFFRACTIONr_chiral_restr0.2460.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212701
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1891.52342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17323773
X-RAY DIFFRACTIONr_scbond_it3.79831277
X-RAY DIFFRACTIONr_scangle_it6.094.51184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.331→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 72 -
Rwork0.276 2519 -
all-2519 -
obs--98 %

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