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- PDB-3st8: Crystal structure of GlmU from Mycobacterium tuberculosis in comp... -

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Basic information

Entry
Database: PDB / ID: 3st8
TitleCrystal structure of GlmU from Mycobacterium tuberculosis in complex with COENZYME A, GLUCOSAMINE 1-PHOSPHATE 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


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
COENZYME A / Chem-GP1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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. / Prakash, B.
History
DepositionJul 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
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 / pdbx_struct_conn_angle / struct_conn / 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 / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)54,1988
Polymers52,4671
Non-polymers1,7317
Water9,530529
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)162,59424
Polymers157,4003
Non-polymers5,19421
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 area23160 Å2
ΔGint-146 kcal/mol
Surface area49970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.312, 110.312, 360.537
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-497-

MG

21A-500-

MG

31A-501-

MG

41A-656-

HOH

51A-710-

HOH

61A-758-

HOH

71A-800-

HOH

81A-1029-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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
#4: Sugar ChemComp-GP1 / 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 1-PHOSPHATE / 1-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-1-O-phosphono-D-glucose / 2-amino-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 259.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-Glcp1PO3NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 535 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 529 / 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: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-Cl, pH-8.5, 2% Tacsimate, 18% PEG 3350, VAPOR DIFFUSION, 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: 432608 / Rmerge(I) obs: 0.053 / D res high: 1.98 Å / Num. obs: 58849 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.8719.7174097.910.021
6.278.87127199.710.024
5.126.27161699.910.026
4.445.12187599.210.025
3.974.44212699.710.029
3.623.97233899.910.033
3.353.62252999.910.036
3.143.35271010010.041
2.963.14287410010.047
2.812.96307210010.056
2.682.81317410010.068
2.562.68331710010.079
2.462.56348610010.094
2.372.46361410010.109
2.292.37372299.910.121
2.222.29382799.910.142
2.152.22398899.810.171
2.092.15405999.910.205
2.042.09420410010.252
1.982.04430799.210.307
ReflectionResolution: 1.98→19.71 Å / Num. all: 58954 / Num. obs: 58849 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 30.049 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.057 / Net I/σ(I): 25.88
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
1.98-2.040.2490.3076.2631164434143070.3399.2
2.04-2.090.2010.2527.7331283420542040.27100
2.09-2.150.1630.2059.4830217406340590.2299.9
2.15-2.220.1380.17111.2729629399439880.18399.8
2.22-2.290.1120.14213.2428481383038270.15399.9
2.29-2.370.0930.12115.2627752372637220.1399.9
2.37-2.460.0870.10916.726923361536140.117100
2.46-2.560.0720.09419.3225920348634860.101100
2.56-2.680.0580.07922.6524663331833170.085100
2.68-2.810.0460.06826.3523570317531740.073100
2.81-2.960.0360.05631.2222745307230720.06100
2.96-3.140.030.04736.6421211287528740.051100
3.14-3.350.0260.04141.4519815271127100.045100
3.35-3.620.0210.03646.3718369253225290.03999.9
3.62-3.970.0180.03351.3416832234123380.03599.9
3.97-4.440.0160.02954.7415218213221260.03299.7
4.44-5.120.0140.02558.3213430189018750.02799.2
5.12-6.270.0140.02655.5911614161716160.02899.9
6.27-8.870.0120.02458.568975127512710.02599.7
8.870.010.02161.1747977567400.02397.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→19.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1945 / WRfactor Rwork: 0.1647 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8829 / SU B: 2.363 / SU ML: 0.068 / SU R Cruickshank DPI: 0.1056 / SU Rfree: 0.1076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1017 1.7 %RANDOM
Rwork0.1674 ---
obs0.1681 58765 99.82 %-
all-58954 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 500 Å2 / Biso mean: 26.3707 Å2 / Biso min: 6.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 107 529 4115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0213640
X-RAY DIFFRACTIONr_angle_refined_deg2.6791.9914987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34423.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32315539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4831531
X-RAY DIFFRACTIONr_chiral_restr0.3930.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212701
X-RAY DIFFRACTIONr_mcbond_it1.6161.52347
X-RAY DIFFRACTIONr_mcangle_it2.65323781
X-RAY DIFFRACTIONr_scbond_it4.32431293
X-RAY DIFFRACTIONr_scangle_it6.8074.51206
LS refinement shellResolution: 1.984→2.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 85 -
Rwork0.218 4152 -
all-4237 -
obs--98.9 %

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