[English] 日本語
Yorodumi
- PDB-3foq: Crystal structure of N-acetylglucosamine-1-phosphate uridyltransf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3foq
TitleCrystal structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group.
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / ACETYLTRANSFERASE / BIFUNCTIONAL / PYROPHOSPHORYLASE / ROSSMANN-LIKE FOLD / LEFT-HANDED-BETA-HELIX / TRIMER / Acyltransferase / Cell shape / Cell wall biogenesis/degradation / Cytoplasm / Magnesium / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Peptidoglycan synthesis
Function / homology
Function and homology information


entry of bacterium into host cell / 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 / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process ...entry of bacterium into host cell / 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 / 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
Bifunctional protein GlmU / Bifunctional protein GlmU
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.41 Å
AuthorsVerma, S.K. / Prakash, B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group.
Authors: Verma, S.K. / Jaiswal, M. / Kumar, N. / Parikh, A. / Nandicoori, V.K. / Prakash, B.
History
DepositionDec 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1115
Polymers52,7271
Non-polymers3844
Water00
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)159,33415
Polymers158,1813
Non-polymers1,15312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area12000 Å2
ΔGint-55 kcal/mol
Surface area51600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)285.700, 285.700, 285.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

-
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: 52726.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: glmU, MRA_1026, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M Ammonium sulphate, 25mM MES, 5% Glycerol, 5mM MgCL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR345 / Detector: IMAGE PLATE / Date: Sep 24, 2007 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3.41→50 Å / Num. obs: 26978 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.911 Å2 / Rmerge(I) obs: 0.194
Reflection shellResolution: 3.5→3.59 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 16523 / Num. unique obs: 1785 / % possible all: 97.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.78 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.41 Å49 Å
Translation3.41 Å49 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.41→48.97 Å / Cor.coef. Fo:Fc: 0.801 / Cor.coef. Fo:Fc free: 0.742 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.229 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.811 / SU B: 22.128 / SU ML: 0.361 / SU R Cruickshank DPI: 0.424 / SU Rfree: 0.358 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32149 1349 5 %RANDOM
Rwork0.28541 ---
obs0.2872 25629 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 230.14 Å2 / Biso mean: 49.321 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 3.41→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 20 0 3186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0213227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.9654415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.995433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25523.136118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88615470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2511526
X-RAY DIFFRACTIONr_chiral_restr0.1230.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.21262
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22173
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7081.52213
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.21123474
X-RAY DIFFRACTIONr_scbond_it9.23631108
X-RAY DIFFRACTIONr_scangle_it13.4944.5941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.413→3.502 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 86 -
Rwork0.37 1647 -
all-1733 -
obs--100 %

+
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