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- PDB-9d9m: Crystal structure of MurC from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 9d9m
TitleCrystal structure of MurC from Pseudomonas aeruginosa in complex (sulfate bound)
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / SSGCID / structural genomics / Seattle Structural Genomics Center for Infectious Disease / MurC
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 speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 DirectorS10 OD030394 United States
CitationJournal: To be published
Title: Crystal structure of MurC from Pseudomonas aeruginosa in complex (sulfate bound)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,01813
Polymers33,9251
Non-polymers1,09212
Water1,17165
1
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)70,03526
Polymers67,8512
Non-polymers2,18424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_465-x-1,-y+1,z1
Buried area6630 Å2
ΔGint-301 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.328, 108.328, 264.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 33925.430 Da / Num. of mol.: 1 / Fragment: R16-R322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: murC, PA4411 / Plasmid: PsaeA.00137.b.B5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HW02, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 5.73 Å3/Da / Density % sol: 78.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.50 M ammonium sulfate, 0.1 M HEPES pH 7.5. PsaeA.00137.b.B5.PW37941 at 22.5 mg/mL. plate 14333 well B8 drop 1. Puck: PSL-1111, Cryo: 2.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 3, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.32→132.45 Å / Num. obs: 33441 / % possible obs: 96.6 % / Redundancy: 16 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.029 / Rrim(I) all: 0.116 / Χ2: 1.01 / Net I/σ(I): 17.1 / Num. measured all: 535069
Reflection shellResolution: 2.32→2.38 Å / % possible obs: 100 % / Redundancy: 15.4 % / Rmerge(I) obs: 2.274 / Num. measured all: 38644 / Num. unique obs: 2510 / CC1/2: 0.777 / Rpim(I) all: 0.596 / Rrim(I) all: 2.352 / Χ2: 1.02 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→68.44 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1645 4.93 %
Rwork0.1975 --
obs0.1983 33386 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→68.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 56 65 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072380
X-RAY DIFFRACTIONf_angle_d0.8223241
X-RAY DIFFRACTIONf_dihedral_angle_d12.922840
X-RAY DIFFRACTIONf_chiral_restr0.052370
X-RAY DIFFRACTIONf_plane_restr0.018418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.390.40151660.37742651X-RAY DIFFRACTION100
2.39-2.470.35471490.31182704X-RAY DIFFRACTION100
2.47-2.550.34971370.26882691X-RAY DIFFRACTION100
2.55-2.660.2761410.23292681X-RAY DIFFRACTION100
2.66-2.780.27171040.22232224X-RAY DIFFRACTION81
2.78-2.920.2631250.22692711X-RAY DIFFRACTION100
2.92-3.110.31241420.27212711X-RAY DIFFRACTION100
3.11-3.350.21131380.22272723X-RAY DIFFRACTION100
3.35-3.680.22851250.18872267X-RAY DIFFRACTION82
3.68-4.220.19941240.17232639X-RAY DIFFRACTION95
4.22-5.310.13871380.1452801X-RAY DIFFRACTION100
5.31-68.440.18441560.18572938X-RAY DIFFRACTION100
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3333-0.2822-0.12490.66070.05970.2983-0.1401-0.2220.16870.09380.1699-0.2933-0.03440.39380.5019-0.0499-0.04380.5907-0.01630.6207-31.871557.634114.6333
20.83320.2105-0.1821.761-0.47690.85050.01390.06070.0430.03330.01520.00960.10950.09190.51670.0236-0.01220.41540.05850.4679-51.402834.16719.4555
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 312 )

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