[English] 日本語
Yorodumi
- PDB-7d1i: Crystal structure of acinetobacter baumannii MurG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d1i
TitleCrystal structure of acinetobacter baumannii MurG
ComponentsUDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
KeywordsTRANSFERASE / undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase Acinetobacter baumannii
Function / homology
Function and homology information


undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase / undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity / UDP-N-acetyl-D-glucosamine:N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol 4-beta-N-acetylglucosaminlytransferase activity / lipid glycosylation / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / plasma membrane
Similarity search - Function
N-acetylglucosaminyltransferase, MurG / Glycosyl transferase, family 28, C-terminal / Glycosyltransferase family 28, N-terminal domain / Glycosyltransferase family 28 N-terminal domain / Glycosyltransferase family 28 C-terminal domain
Similarity search - Domain/homology
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.487 Å
AuthorsPark, H.H. / Jeong, k.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Iucrj / Year: 2021
Title: Putative hexameric glycosyltransferase functional unit revealed by the crystal structure of Acinetobacter baumannii MurG
Authors: Jung, K.H. / Kwon, S. / Kim, C.M. / Lee, J.H. / Park, H.H.
History
DepositionSep 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
B: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
C: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase


Theoretical massNumber of molelcules
Total (without water)118,4303
Polymers118,4303
Non-polymers00
Water00
1
A: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
B: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
C: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase

A: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
B: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
C: UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase


Theoretical massNumber of molelcules
Total (without water)236,8606
Polymers236,8606
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18550 Å2
ΔGint-114 kcal/mol
Surface area81170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.909, 182.909, 156.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase / Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase


Mass: 39476.723 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: murG, BGC29_11725 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1E3MA13, undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.53 Å3/Da / Density % sol: 77.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH8.8, 2.6M Sodium chloride 0.15M Ca(OAc)2

-
Data collection

DiffractionMean temperature: 104.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.487→48.264 Å / Num. obs: 31262 / % possible obs: 90.8 % / Redundancy: 8.2 % / Rsym value: 0.083 / Net I/σ(I): 9.45
Reflection shellResolution: 3.487→3.57 Å / Num. unique obs: 1765 / Rsym value: 0.489

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F0K

1f0k


Resolution: 3.487→48.259 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.832 / Cross valid method: FREE R-VALUE / ESU R Free: 0.555
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2976 1511 4.843 %
Rwork0.2606 29690 -
all0.262 --
obs-31201 90.611 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.562 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å2-0 Å2-0 Å2
2--0.001 Å2-0 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 3.487→48.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7702 0 0 0 7702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0137838
X-RAY DIFFRACTIONr_bond_other_d0.0350.0177578
X-RAY DIFFRACTIONr_angle_refined_deg2.051.63810645
X-RAY DIFFRACTIONr_angle_other_deg2.361.56617580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66151014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84823.768345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.433151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4811534
X-RAY DIFFRACTIONr_chiral_restr0.1280.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028715
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021447
X-RAY DIFFRACTIONr_nbd_refined0.2510.21966
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2780.27917
X-RAY DIFFRACTIONr_nbtor_refined0.1950.23861
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.24281
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1510.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.232
X-RAY DIFFRACTIONr_nbd_other0.2880.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3740.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2070.21
X-RAY DIFFRACTIONr_mcbond_it5.5296.7234080
X-RAY DIFFRACTIONr_mcbond_other5.5286.7234079
X-RAY DIFFRACTIONr_mcangle_it8.92810.0715086
X-RAY DIFFRACTIONr_mcangle_other8.92710.0715087
X-RAY DIFFRACTIONr_scbond_it5.1646.9193758
X-RAY DIFFRACTIONr_scbond_other5.1646.9193759
X-RAY DIFFRACTIONr_scangle_it8.68810.2855559
X-RAY DIFFRACTIONr_scangle_other8.68710.2845560
X-RAY DIFFRACTIONr_lrange_it12.90781.8128640
X-RAY DIFFRACTIONr_lrange_other12.90881.8148641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.487-3.5770.3461100.33818230.33924740.7570.76378.13260.332
3.577-3.6750.331920.31118560.31224240.8220.8180.3630.298
3.675-3.7810.324940.30318880.30523780.8190.81783.34740.283
3.781-3.8960.314960.28418730.28623010.8630.86685.57150.267
3.896-4.0230.279970.28518400.28522380.9030.88486.55050.263
4.023-4.1630.274930.25118160.25221620.890.89988.29790.231
4.163-4.3190.314820.24417590.24720850.8780.90288.29740.215
4.319-4.4940.229810.21916900.21919920.9290.9388.90560.195
4.494-4.6920.262780.21216800.21419360.9090.93590.80580.187
4.692-4.9190.255840.23416630.23518750.9240.92693.17330.21
4.919-5.1820.328990.25315910.25817620.8890.90995.91370.229
5.182-5.4920.397780.27315760.27816920.8640.89897.75410.247
5.492-5.8660.297690.28115020.28115850.8820.89299.11670.254
5.866-6.3280.316690.2914140.29114880.8830.87599.6640.256
6.328-6.920.341690.26412970.26713680.8750.90899.85380.233
6.92-7.7170.258470.24312160.24412630.8960.9241000.222
7.717-8.8740.256540.22510770.22711320.930.9499.91170.217
8.874-10.7770.235500.1959170.1979680.950.9699.89670.197
10.777-14.8750.243370.2527400.2517780.9460.92799.87150.257
14.875-48.2640.482320.4244720.4285100.810.81198.82350.396

+
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