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- PDB-6ge9: Structure of Mycobacterium tuberculosis GlmU bound to Glc-1P and ... -

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Basic information

Entry
Database: PDB / ID: 6ge9
TitleStructure of Mycobacterium tuberculosis GlmU bound to Glc-1P and Ac-CoA
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / GlmU / Glc-1P / Ac-CoA
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 wall organization / cell morphogenesis / 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 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 / Hexapeptide repeat / 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 proteins / Hexapeptide repeat / 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 / 1-O-phosphono-alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsCraggs, P.D. / Mouilleron, S. / Rejzek, M. / de Chiara, C. / Young, R.J. / Field, R.A. / Argyrou, A. / de Carvalho, L.P.S.
CitationJournal: Biochemistry / Year: 2018
Title: The Mechanism of Acetyl Transfer Catalyzed by Mycobacterium tuberculosis GlmU.
Authors: Craggs, P.D. / Mouilleron, S. / Rejzek, M. / de Chiara, C. / Young, R.J. / Field, R.A. / Argyrou, A. / de Carvalho, L.P.S.
History
DepositionApr 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1309
Polymers51,6381
Non-polymers1,4928
Water1,67593
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)159,39127
Polymers154,9133
Non-polymers4,47724
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
Buried area18370 Å2
ΔGint-36 kcal/mol
Surface area54650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.753, 109.753, 364.894
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-501-

MG

21A-653-

HOH

31A-677-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Bifunctional protein GlmU


Mass: 51637.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra) (bacteria)
Strain: ATCC 25177 / H37Ra / Gene: glmU, MRA_1026 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U161, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#3: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 100 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.1 Å3/Da / Density % sol: 69.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.05 M ADA pH 6.8, 5.7% PEG 550 MME, 32.1% PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.26→47.71 Å / Num. obs: 40178 / % possible obs: 98.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.07 / Num. unique obs: 3861 / Rpim(I) all: 0.46 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G87

4g87


Resolution: 2.26→47.126 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 1928 4.88 %
Rwork0.2434 --
obs0.245 39547 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→47.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 94 93 3640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023630
X-RAY DIFFRACTIONf_angle_d0.5674962
X-RAY DIFFRACTIONf_dihedral_angle_d11.0162868
X-RAY DIFFRACTIONf_chiral_restr0.045604
X-RAY DIFFRACTIONf_plane_restr0.003644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2596-2.31610.53151660.50722560X-RAY DIFFRACTION96
2.3161-2.37870.47611330.47722639X-RAY DIFFRACTION97
2.3787-2.44870.46831380.45682603X-RAY DIFFRACTION98
2.4487-2.52770.44551330.44152625X-RAY DIFFRACTION98
2.5277-2.6180.41121270.41322636X-RAY DIFFRACTION97
2.618-2.72290.46531360.39242664X-RAY DIFFRACTION98
2.7229-2.84680.43841160.37052674X-RAY DIFFRACTION98
2.8468-2.99680.39231450.3212673X-RAY DIFFRACTION98
2.9968-3.18460.3561220.29932710X-RAY DIFFRACTION99
3.1846-3.43040.2661540.25392723X-RAY DIFFRACTION100
3.4304-3.77540.26341520.21672685X-RAY DIFFRACTION99
3.7754-4.32140.21951410.1762745X-RAY DIFFRACTION100
4.3214-5.44330.17341220.15952775X-RAY DIFFRACTION99
5.4433-47.13670.20261430.17622907X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66760.4125-0.30220.1961-0.02360.28370.25650.4680.634-0.0535-0.15560.0602-0.0515-0.7064-0.01430.3676-0.07750.00860.8808-0.10360.564626.0209-37.078328.4039
20.0339-0.0367-0.00560.47390.27380.5956-0.30860.4968-0.03340.24650.12980.32230.4986-1.0361-0.04310.3874-0.1354-0.00931.2275-0.09180.603819.1156-37.173624.1008
30.5554-0.53840.03180.9707-0.05271.2416-0.0152-0.07090.10080.3717-0.0818-0.06990.0852-0.7292-0.13840.3298-0.16590.07120.8937-0.08410.359625.801-35.196145.2736
40.3961-0.44980.34730.0591-0.080.2933-0.0184-0.13480.09380.11840.0339-0.25750.3573-0.2956-0.00270.2815-0.09430.03830.408-0.02910.313541.541-39.922931.1004
50.30160.5051-0.19960.5272-0.33610.8268-0.13440.17710.0272-0.09110.055-0.07940.4642-0.281800.4423-0.04050.01750.3579-0.05120.389848.2696-43.9225-3.3829
60.1054-0.22240.00530.4925-0.4990.75170.16040.27540.2983-0.3791-0.0945-0.04670.0106-0.14150.00060.711-0.09120.13440.4829-0.03570.581160.5035-32.7564-24.6571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 88 )
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 210 )
4X-RAY DIFFRACTION4chain 'A' and (resid 211 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 418 )
6X-RAY DIFFRACTION6chain 'A' and (resid 419 through 478 )

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