[English] 日本語
Yorodumi
- PDB-5vvw: Structure of MurC from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vvw
TitleStructure of MurC from Pseudomonas aeruginosa
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / Pseudomonas aeruginosa / SSGCID / Beryllium / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain ...UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Structure of MurC from Pseudomonas aeruginosa
Authors: Horanyi, P.S. / Mayclin, S.J. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
B: UDP-N-acetylmuramate--L-alanine ligase
C: UDP-N-acetylmuramate--L-alanine ligase
D: UDP-N-acetylmuramate--L-alanine ligase
E: UDP-N-acetylmuramate--L-alanine ligase
F: UDP-N-acetylmuramate--L-alanine ligase
G: UDP-N-acetylmuramate--L-alanine ligase
H: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,19815
Polymers270,7648
Non-polymers4347
Water15,799877
1
A: UDP-N-acetylmuramate--L-alanine ligase
F: UDP-N-acetylmuramate--L-alanine ligase
G: UDP-N-acetylmuramate--L-alanine ligase
H: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,6929
Polymers135,3824
Non-polymers3105
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylmuramate--L-alanine ligase
C: UDP-N-acetylmuramate--L-alanine ligase
D: UDP-N-acetylmuramate--L-alanine ligase
E: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5066
Polymers135,3824
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)284.820, 109.400, 108.580
Angle α, β, γ (deg.)90.00, 112.38, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 33845.449 Da / Num. of mol.: 8 / Fragment: UNP residues 16-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: murC, PA4411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 3 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Morpheus A2: 60mM Divalents, (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate), 100mM Imidazole; MES monohydrate (acid), 20% v/v Ethylene glycol; 10 % w/v PEG 8000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.3→29.812 Å / Num. obs: 136319 / % possible obs: 99.73 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.46

-
Processing

Software
NameVersionClassification
PHENIX(dev_2744: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HV4

4hv4


Resolution: 2.3→29.812 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.92
RfactorNum. reflection% reflection
Rfree0.203 2006 1.47 %
Rwork0.1888 --
obs0.189 136319 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17923 0 28 877 18828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818473
X-RAY DIFFRACTIONf_angle_d0.91625186
X-RAY DIFFRACTIONf_dihedral_angle_d21.3466553
X-RAY DIFFRACTIONf_chiral_restr0.0562990
X-RAY DIFFRACTIONf_plane_restr0.0063324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.32411450.28139555X-RAY DIFFRACTION100
2.3575-2.42120.25931450.25769557X-RAY DIFFRACTION100
2.4212-2.49240.31091400.24479582X-RAY DIFFRACTION100
2.4924-2.57280.24711360.23779522X-RAY DIFFRACTION100
2.5728-2.66470.2381420.22479610X-RAY DIFFRACTION100
2.6647-2.77130.27281490.21699569X-RAY DIFFRACTION100
2.7713-2.89740.23651440.20559577X-RAY DIFFRACTION100
2.8974-3.050.22591430.20369619X-RAY DIFFRACTION100
3.05-3.24090.25741440.2049614X-RAY DIFFRACTION100
3.2409-3.49070.2021420.19099575X-RAY DIFFRACTION100
3.4907-3.84140.18781430.17689608X-RAY DIFFRACTION100
3.8414-4.39570.1731450.15099641X-RAY DIFFRACTION100
4.3957-5.53230.14751450.14799695X-RAY DIFFRACTION100
5.5323-29.81460.14661430.16799589X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 50.9837 Å / Origin y: -3.0553 Å / Origin z: -37.703 Å
111213212223313233
T0.2044 Å2-0.0178 Å2-0.0041 Å2-0.2452 Å20.015 Å2--0.217 Å2
L0.2001 °2-0.0725 °2-0.0065 °2-0.2441 °20.0493 °2--0.1871 °2
S0.0266 Å °0.0304 Å °-0.0118 Å °-0.0105 Å °-0.0119 Å °-0.0498 Å °0.0143 Å °0.0286 Å °-0.0155 Å °
Refinement TLS groupSelection details: all

+
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