[English] 日本語
Yorodumi
- PDB-8zov: The crystal structures of MurK in complex with glucose from Clost... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zov
TitleThe crystal structures of MurK in complex with glucose from Clostridium acetobutylicum
ComponentsN-acetylmuramic acid/N-acetylglucosamine kinase
KeywordsTRANSFERASE / N-acetylmuramic acid/N-acetylglucosamine kinase / MurK / Nucleotide-binding
Function / homology
Function and homology information


N-acetylmuramic acid metabolic process / carbohydrate kinase activity / N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / carbohydrate phosphorylation / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / peptidoglycan turnover / ATP binding / cytoplasm
Similarity search - Function
: / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
beta-D-glucopyranose / N-acetylmuramic acid/N-acetylglucosamine kinase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsYang, X.Y. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and biochemical insights into the molecular mechanism of N-acetylglucosamine/N-Acetylmuramic acid kinase MurK from Clostridium acetobutylicum.
Authors: He, X. / Liu, C. / Li, X. / Yang, Q. / Niu, F. / An, L. / Fan, Y. / Li, Y. / Zhou, Z. / Zhou, H. / Yang, X. / Liu, X.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6532
Polymers33,4731
Non-polymers1801
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules

A: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3064
Polymers66,9462
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3410 Å2
ΔGint-10 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.360, 52.140, 53.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-747-

HOH

-
Components

#1: Protein N-acetylmuramic acid/N-acetylglucosamine kinase / MurNAc/GlcNAc kinase / Murein sugar kinase


Mass: 33472.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W) (bacteria)
Gene: murK, CA_C0183 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97ML3, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, N-acetylglucosamine kinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M Tris-HCl pH8.5 1.5 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.42→47.77 Å / Num. obs: 57956 / % possible obs: 99.6 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.027 / Rrim(I) all: 0.095 / Χ2: 1.02 / Net I/σ(I): 15.4 / Num. measured all: 719334
Reflection shellResolution: 1.42→1.46 Å / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 1.385 / Num. measured all: 43086 / Num. unique obs: 4243 / CC1/2: 0.627 / Rpim(I) all: 0.451 / Rrim(I) all: 1.458 / Χ2: 0.81 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→37.73 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 2932 5.07 %
Rwork0.1928 --
obs0.1944 57785 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 12 265 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062318
X-RAY DIFFRACTIONf_angle_d0.8883116
X-RAY DIFFRACTIONf_dihedral_angle_d5.092330
X-RAY DIFFRACTIONf_chiral_restr0.077373
X-RAY DIFFRACTIONf_plane_restr0.006385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.35641600.34142584X-RAY DIFFRACTION100
1.44-1.470.34011470.29992561X-RAY DIFFRACTION100
1.47-1.490.40121440.34182577X-RAY DIFFRACTION100
1.49-1.520.28071370.2292595X-RAY DIFFRACTION100
1.52-1.550.23891140.21842605X-RAY DIFFRACTION100
1.55-1.590.24161190.21212617X-RAY DIFFRACTION100
1.59-1.630.23241100.19552636X-RAY DIFFRACTION100
1.63-1.670.21141290.18782595X-RAY DIFFRACTION100
1.67-1.710.22771400.18792596X-RAY DIFFRACTION100
1.71-1.760.22741580.19052592X-RAY DIFFRACTION100
1.76-1.820.23281240.19222622X-RAY DIFFRACTION100
1.82-1.880.25081360.19772604X-RAY DIFFRACTION100
1.88-1.960.26531430.29972406X-RAY DIFFRACTION92
1.96-2.050.22271390.18862601X-RAY DIFFRACTION100
2.05-2.160.20111700.18252588X-RAY DIFFRACTION100
2.16-2.290.24991380.20492574X-RAY DIFFRACTION98
2.29-2.470.19861540.17912633X-RAY DIFFRACTION100
2.47-2.720.20781280.18312667X-RAY DIFFRACTION100
2.72-3.110.22151490.18612673X-RAY DIFFRACTION100
3.11-3.920.19681400.16652711X-RAY DIFFRACTION100
3.92-37.730.21951530.17682816X-RAY DIFFRACTION100

+
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