[English] 日本語
Yorodumi
- PDB-8vw2: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vw2
TitleCrystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ATP bound)
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ATP bound)
Authors: Seibold, S. / Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,87011
Polymers47,9491
Non-polymers92110
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.456, 69.944, 100.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase


Mass: 47949.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murD, b0088, JW0086 / Plasmid: EscoA.17938.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

-
Non-polymers , 6 types, 153 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, 2% (v/v) DMSO. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. 4 hour ...Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, 2% (v/v) DMSO. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. 4 hour soak in 5 mM ATP. plate 13768 well E4 drop 1 or 2. Puck: PSL-1106, Cryo: direct

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.95→44.85 Å / Num. obs: 30773 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.046 / Rrim(I) all: 0.133 / Χ2: 0.98 / Net I/σ(I): 10.7 / Num. measured all: 240573
Reflection shellResolution: 1.95→2 Å / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 1.151 / Num. measured all: 16660 / Num. unique obs: 2139 / CC1/2: 0.826 / Rpim(I) all: 0.428 / Rrim(I) all: 1.23 / Χ2: 1.05 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5219: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→44.85 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 1528 4.98 %
Rwork0.1696 --
obs0.1723 30654 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 50 143 3456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083375
X-RAY DIFFRACTIONf_angle_d0.9344596
X-RAY DIFFRACTIONf_dihedral_angle_d15.2811242
X-RAY DIFFRACTIONf_chiral_restr0.056537
X-RAY DIFFRACTIONf_plane_restr0.008599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.33271430.25172581X-RAY DIFFRACTION100
2.01-2.080.30011440.22232613X-RAY DIFFRACTION100
2.08-2.170.24841230.1922623X-RAY DIFFRACTION100
2.17-2.270.24511230.17142625X-RAY DIFFRACTION100
2.27-2.390.21211430.16412607X-RAY DIFFRACTION100
2.39-2.540.25831500.17762628X-RAY DIFFRACTION100
2.54-2.730.23121330.18762634X-RAY DIFFRACTION100
2.73-3.010.26351300.17742659X-RAY DIFFRACTION100
3.01-3.440.23381470.16752668X-RAY DIFFRACTION100
3.44-4.340.18961390.14582696X-RAY DIFFRACTION99
4.34-44.850.19631530.16042792X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0030.08880.26370.75740.04041.7374-0.0075-0.1163-0.06780.16410.0286-0.01030.012-0.0351-0.01650.32820.0081-0.00810.26030.01850.2809-4.8663-15.0201-3.3779
21.3269-0.1153-0.50741.36260.5782.12970.02570.0666-0.02760.0338-0.0526-0.02090.0410.04080.02410.2095-0.0002-0.0320.20130.01250.24050.025-23.5486-31.2213
31.61290.37840.50860.94640.06411.26890.02160.0715-0.16090.0720.0601-0.0170.11760.2408-0.07740.26610.02090.00220.42850.01870.262326.3152-18.3261-29.6643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 440 )

+
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