[English] 日本語
Yorodumi
- PDB-3twd: glmuC1 in complex with an antibacterial inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3twd
TitleglmuC1 in complex with an antibacterial inhibitor
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / acetyl transferase / uridyl transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / identical protein binding / membrane / cytosol
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 of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins ...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 of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Nucleotide-diphospho-sugar transferases / Mainly Beta
Similarity search - Domain/homology
Chem-GOB / Bifunctional protein GlmU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLahiri, S. / Otterbein, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: In Vitro Validation of Acetyltransferase Activity of GlmU as an Antibacterial Target in Haemophilus influenzae.
Authors: Buurman, E.T. / Andrews, B. / Gao, N. / Hu, J. / Keating, T.A. / Lahiri, S. / Otterbein, L.R. / Patten, A.D. / Stokes, S.S. / Shapiro, A.B.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Feb 28, 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
B: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1916
Polymers46,9992
Non-polymers1,1914
Water6,990388
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)72,2869
Polymers70,4993
Non-polymers1,7876
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 area13050 Å2
ΔGint-94 kcal/mol
Surface area23260 Å2
MethodPISA
2
B: Bifunctional protein glmU
hetero molecules

B: Bifunctional protein glmU
hetero molecules

B: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2869
Polymers70,4993
Non-polymers1,7876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area13490 Å2
ΔGint-92 kcal/mol
Surface area23130 Å2
MethodPISA
3
A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules

B: Bifunctional protein glmU
hetero molecules

B: Bifunctional protein glmU
hetero molecules

B: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,57218
Polymers140,9986
Non-polymers3,57412
Water1086
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
crystal symmetry operation4_655-x+1,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/21
crystal symmetry operation6_545x-y,x-1,z+1/21
Buried area29530 Å2
ΔGint-214 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.526, 80.526, 139.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-478-

HOH

31B-509-

HOH

-
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: 23499.652 Da / Num. of mol.: 2 / Fragment: UNP residues 233-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glmU, yieA, b3730, JW3708 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ACC7, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOB / 4-({5-[(4-aminophenyl)(phenyl)sulfamoyl]-2,4-dimethoxyphenyl}amino)-4-oxobutanoic acid


Mass: 499.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 19-22% (w/v) PEG3350, 100mM PCTP pH 5.5 and 400mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→69.84 Å / Observed criterion σ(F): 3 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassificationNB
REFMAC5.3.0034refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→69.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.082 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1945 5 %RANDOM
obs-38936 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.8 Å2 / Biso mean: 26.32 Å2 / Biso min: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 80 388 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223514
X-RAY DIFFRACTIONr_bond_other_d0.0020.022298
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9874778
X-RAY DIFFRACTIONr_angle_other_deg0.86635620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61823.803142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41215584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111530
X-RAY DIFFRACTIONr_chiral_restr0.080.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined0.1950.2678
X-RAY DIFFRACTIONr_nbd_other0.2070.22452
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21753
X-RAY DIFFRACTIONr_nbtor_other0.0790.22026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.2148
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.242
X-RAY DIFFRACTIONr_mcbond_it0.841.52323
X-RAY DIFFRACTIONr_mcbond_other0.1991.5946
X-RAY DIFFRACTIONr_mcangle_it1.10223604
X-RAY DIFFRACTIONr_scbond_it2.24731361
X-RAY DIFFRACTIONr_scangle_it3.4474.51174
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 104 -
Rwork0.201 2051 -
all-2155 -
obs--72.88 %
Refinement TLS params.Method: refined / Origin x: 33.8083 Å / Origin y: -0.1358 Å / Origin z: 0.0117 Å
111213212223313233
T-0.028 Å2-0.0004 Å20.0017 Å2--0.0127 Å20.0003 Å2---0.0087 Å2
L0.1017 °20.0032 °20.0055 °2-0.3552 °20.0013 °2--0.0598 °2
S0.0036 Å °-0.0026 Å °-0.0019 Å °0.0032 Å °0.0031 Å °0.0068 Å °0.0021 Å °0.0023 Å °-0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A232 - 453
2X-RAY DIFFRACTION1B232 - 453
3X-RAY DIFFRACTION1A2
4X-RAY DIFFRACTION1B1
5X-RAY DIFFRACTION1A1
6X-RAY DIFFRACTION1B454

+
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://pdbjlvh1.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