[English] 日本語
Yorodumi
- PDB-4qf5: Crystal structure I of MurF from Acinetobacter baumannii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qf5
TitleCrystal structure I of MurF from Acinetobacter baumannii
ComponentsUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
KeywordsLIGASE / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-ananine ligase / MurF
Function / homology
Function and homology information


UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase family, catalytic domain / Mur ligase, N-terminal catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain ...UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase family, catalytic domain / Mur ligase, N-terminal catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase middle domain / Mur-like, catalytic domain superfamily / Mur ligase, central / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / :
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAn, Y.J. / Jeong, C.S. / Cha, S.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF
Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Yu, J.H. / Chung, K.M.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
B: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6178
Polymers103,5052
Non-polymers1,1126
Water0
1
A: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3084
Polymers51,7531
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3084
Polymers51,7531
Non-polymers5563
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.559, 89.716, 126.896
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase


Mass: 51752.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: ABBFA_000315 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli)
References: UniProt: B7GVN5, UniProt: A0A0J9X1Z8*PLUS, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 295 K / Method: micro-batch crystallization method / pH: 8.5
Details: 0.16M Magnesium Chloride, 0.08M Tris-HCl pH 8.5, 24%(w/v) polyethylene glycol(PEG) 4,000, 20%(w/v) glycerol, micro-batch crystallization method, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24942 / % possible obs: 99.7 %
Reflection shellResolution: 2.8→2.85 Å / % possible all: 92.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→37.439 Å / SU ML: 0.36 / σ(F): 1.54 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1236 5.14 %
Rwork0.1919 --
obs0.1949 24046 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→37.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6913 0 66 0 6979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017107
X-RAY DIFFRACTIONf_angle_d1.2469651
X-RAY DIFFRACTIONf_dihedral_angle_d13.672573
X-RAY DIFFRACTIONf_chiral_restr0.0321100
X-RAY DIFFRACTIONf_plane_restr0.0041264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.91210.31491180.2446240194
2.9121-3.04450.32091270.2425246395
3.0445-3.2050.2731360.2317252697
3.205-3.40570.2881350.2059252898
3.4057-3.66840.25271460.1921254198
3.6684-4.03720.22731490.1782256399
4.0372-4.62050.23291360.1655256299
4.6205-5.81780.21381450.1744259499
5.8178-37.44250.22821440.1749263298

+
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