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- PDB-9ir6: Crystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (M... -

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Basic information

Entry
Database: PDB / ID: 9ir6
TitleCrystal structure of UDP-N-acetylmuramic Acid L-alanine ligase (MurC) from Roseburia faecis in complex with UNAM
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / MurC / peptidoglycan / UNAM
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
Chem-EPZ / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesRoseburia faecis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2498
Polymers100,6422
Non-polymers1,6076
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.982, 76.688, 94.943
Angle α, β, γ (deg.)90.00, 97.46, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M BIS-TRIS pH5.7, 15%(w/v) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.43→62.43 Å / Num. obs: 39944 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 2.43→2.56 Å / Num. unique obs: 39944 / CC1/2: 0.846

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→47.07 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 2092 5.24 %
Rwork0.1884 --
obs0.1905 39896 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 4 261 7423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.517
X-RAY DIFFRACTIONf_dihedral_angle_d12.8162628
X-RAY DIFFRACTIONf_chiral_restr0.0431125
X-RAY DIFFRACTIONf_plane_restr0.0051278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.490.3541060.26852541X-RAY DIFFRACTION98
2.49-2.550.33651510.25162477X-RAY DIFFRACTION98
2.55-2.620.27711340.24042504X-RAY DIFFRACTION98
2.62-2.690.30581400.23442492X-RAY DIFFRACTION98
2.69-2.780.32841400.24512497X-RAY DIFFRACTION98
2.78-2.880.28461360.2312499X-RAY DIFFRACTION99
2.88-30.29441510.22692514X-RAY DIFFRACTION99
3-3.130.27011150.21592535X-RAY DIFFRACTION99
3.13-3.30.23481500.21222486X-RAY DIFFRACTION99
3.3-3.50.23931260.19082537X-RAY DIFFRACTION99
3.5-3.770.23761530.17192533X-RAY DIFFRACTION99
3.77-4.150.16441610.15152509X-RAY DIFFRACTION99
4.15-4.750.17721480.14022550X-RAY DIFFRACTION99
4.75-5.990.1781350.16752562X-RAY DIFFRACTION99
5.99-47.070.19271460.15912568X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 13.8934 Å / Origin y: 8.1594 Å / Origin z: 24.8366 Å
111213212223313233
T0.2563 Å2-0.0045 Å2-0.0154 Å2-0.2412 Å2-0.0112 Å2--0.2511 Å2
L0.0112 °2-0.0163 °20.0199 °2--0.0389 °2-0.0164 °2--0.0275 °2
S-0.0154 Å °0.0149 Å °0.0104 Å °-0.0068 Å °-0.0038 Å °0.0088 Å °-0.0039 Å °0.0183 Å °-0 Å °
Refinement TLS groupSelection details: all

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