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- PDB-9ir5: Crystal structure of apo-form UDP-N-acetylmuramic Acid L-alanine ... -

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Basic information

Entry
Database: PDB / ID: 9ir5
TitleCrystal structure of apo-form UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Roseburia faecis
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / peptidoglycan
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 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 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
UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesRoseburia faecis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsWang, Y.X. / Du, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Unusual MurC Ligase and Peptidoglycan Discovered in Lachnospiraceae Using a Fluorescent L-Amino Acid Based Selective Labeling Probe.
Authors: Du, Y. / Wang, Y. / Yang, M. / Lin, L. / Zhang, J. / Huang, Z. / Liu, C. / Liu, S. / Ma, J. / Yang, C. / Wang, W.
History
DepositionJul 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3832
Polymers50,3211
Non-polymers621
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.138, 107.342, 61.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 50321.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia faecis (bacteria) / Gene: murC, ERS852420_02569, GMD30_02630, M72_17401 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M6X1Q9, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 15%(w/v) polyethylene glycol (PEG) 20000, 100 mM HEPES/Sodium hydroxide pH7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.36→65.23 Å / Num. obs: 20564 / % possible obs: 90.2 % / Redundancy: 5.1 % / CC1/2: 0.996 / Net I/σ(I): 10.8
Reflection shellResolution: 2.36→2.49 Å / Num. unique obs: 20564 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
AutoProcessdata reduction
AutoProcessdata scaling
AutoProcessphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→65.23 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1011 4.93 %
Rwork0.1887 --
obs0.1903 20515 90.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→65.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3539 0 0 131 3670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.428
X-RAY DIFFRACTIONf_dihedral_angle_d14.1071319
X-RAY DIFFRACTIONf_chiral_restr0.069555
X-RAY DIFFRACTIONf_plane_restr0.033639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.490.38591600.27013019X-RAY DIFFRACTION100
2.49-2.610.36641150.26252297X-RAY DIFFRACTION98
2.72-2.850.2839890.22971766X-RAY DIFFRACTION99
2.85-3.140.24761720.21923035X-RAY DIFFRACTION100
3.14-3.590.22791470.19533075X-RAY DIFFRACTION99
3.59-4.520.17881530.16043101X-RAY DIFFRACTION100
4.52-65.230.17851750.16053211X-RAY DIFFRACTION99

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