[English] 日本語
Yorodumi
- PDB-6ge9: Structure of Mycobacterium tuberculosis GlmU bound to Glc-1P and ... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Acetyl-CoA


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


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


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more