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- PDB-9s8i: Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC)... -

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Basic information

Entry
Database: PDB / ID: 9s8i
TitleCrystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsBIOSYNTHETIC PROTEIN / Dimer / Inhibitor
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Chem-WIR / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDiaz-Saez, L. / Lloyd, A.J. / Wang, Y. / Todd, M.H. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Warwick United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of UDP-N-acetylmuramate-L-alanine ligase (MurC) from Pseudomonas aeruginosa in complex with compound OSA_001176 (WYH78)
Authors: Diaz-Saez, L. / Lloyd, A.J. / Wang, Y. / Todd, M.H. / Dowson, C.G.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)108,51931
Polymers105,8132
Non-polymers2,70629
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint9 kcal/mol
Surface area36570 Å2
Unit cell
Length a, b, c (Å)60.579, 99.108, 192.556
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 52906.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: murC, PA4411 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase

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Non-polymers , 7 types, 382 molecules

#2: Chemical ChemComp-WIR / (1R,2S)-1-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl)amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2,3-dihydro-1H-inden-2-ol


Mass: 418.495 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 20mg/mL. Reservoir: 0.1 M MES pH 6.5, and 12 % (w/v) PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.3→88.28 Å / Num. obs: 52491 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Χ2: 0.93 / Net I/σ(I): 20.5
Reflection shellResolution: 2.3→2.37 Å / % possible obs: 100 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.523 / Num. measured all: 52193 / Num. unique obs: 4467 / CC1/2: 0.925 / Rpim(I) all: 0.158 / Rrim(I) all: 0.546 / Χ2: 0.86 / Net I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→88.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.098 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23926 2705 5.2 %RANDOM
Rwork0.18839 ---
obs0.19102 49711 100 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20 Å2
2---0.95 Å2-0 Å2
3---0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.3→88.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6938 0 176 353 7467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0127473
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167283
X-RAY DIFFRACTIONr_angle_refined_deg1.281.83810160
X-RAY DIFFRACTIONr_angle_other_deg0.4991.75916680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5485962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.225577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.117101224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.394.5283683
X-RAY DIFFRACTIONr_mcbond_other5.394.5293683
X-RAY DIFFRACTIONr_mcangle_it6.9558.1264611
X-RAY DIFFRACTIONr_mcangle_other6.9548.1274612
X-RAY DIFFRACTIONr_scbond_it6.3645.0063790
X-RAY DIFFRACTIONr_scbond_other6.3385.0023767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7138.9455482
X-RAY DIFFRACTIONr_long_range_B_refined10.6643.518056
X-RAY DIFFRACTIONr_long_range_B_other10.66643.58003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 204 -
Rwork0.219 3592 -
obs--99.97 %

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