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- PDB-9d9k: Crystal structure of MurC from Pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 9d9k
TitleCrystal structure of MurC from Pseudomonas aeruginosa in complex with inhibitor M17
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE/INHIBITOR / SSGCID / structural genomics / Seattle Structural Genomics Center for Infectious Disease / MurC / LIGASE-INHIBITOR complex
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: 2.63 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 with inhibitor M17
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 9, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,71015
Polymers33,9251
Non-polymers1,78514
Water57632
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)71,42130
Polymers67,8512
Non-polymers3,57028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_465-x-1,-y+1,z1
Buried area7500 Å2
ΔGint-300 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.711, 108.711, 265.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-414-

A1A23

21A-414-

A1A23

31A-414-

A1A23

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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: Chemical ChemComp-A1A23 / 2-{[(4-amino-5,6-dimethylthieno[2,3-d]pyrimidin-2-yl)methyl]sulfanyl}pyridine-3-carboxylic acid


Mass: 346.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N4O2S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 5.77 Å3/Da / Density % sol: 78.68 %
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. Overnight soak with 5mM compound M17 in 1.0 M ammonium sulfate, 0.1M Hepes 7.5. plate 14333 well B8 drop ...Details: 0.50 M ammonium sulfate, 0.1 M HEPES pH 7.5. PsaeA.00137.b.B5.PW37941 at 22.5 mg/mL. Overnight soak with 5mM compound M17 in 1.0 M ammonium sulfate, 0.1M Hepes 7.5. plate 14333 well B8 drop 1. Puck: PSL-1208, Cryo: 2.5M ammonium sulfate + 5mM M17

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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: 2.63→132.52 Å / Num. obs: 24139 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.998 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.065 / Rrim(I) all: 0.245 / Χ2: 0.99 / Net I/σ(I): 10.7 / Num. measured all: 338789
Reflection shellResolution: 2.63→2.7 Å / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 3.104 / Num. measured all: 26567 / Num. unique obs: 1754 / CC1/2: 0.657 / Rpim(I) all: 0.815 / Rrim(I) all: 3.211 / Χ2: 0.96 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→68.56 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1246 5.17 %
Rwork0.2047 --
obs0.2062 24098 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→68.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 102 32 2430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072430
X-RAY DIFFRACTIONf_angle_d0.8253313
X-RAY DIFFRACTIONf_dihedral_angle_d13.784880
X-RAY DIFFRACTIONf_chiral_restr0.049370
X-RAY DIFFRACTIONf_plane_restr0.008442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.740.43711270.38932502X-RAY DIFFRACTION100
2.74-2.860.33791690.30522472X-RAY DIFFRACTION100
2.86-3.010.30111290.23912499X-RAY DIFFRACTION100
3.01-3.20.27191260.24582517X-RAY DIFFRACTION100
3.2-3.450.32731190.2652508X-RAY DIFFRACTION100
3.45-3.790.23781310.17742532X-RAY DIFFRACTION100
3.79-4.340.22181420.17492553X-RAY DIFFRACTION100
4.34-5.470.16111380.15832569X-RAY DIFFRACTION100
5.47-68.560.19741650.19282700X-RAY DIFFRACTION100
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)
10.59180.2095-0.01340.50570.23750.425-0.0647-0.33010.0586-0.03520.1209-0.3562-0.13710.305800.5457-0.02130.00070.6905-0.01790.6436-29.747456.877712.8889
20.70481.1565-0.49961.9205-0.7220.94150.0238-0.0940.11810.14550.0881-0.07150.14930.186-00.5250.04790.00830.49610.03910.5406-47.746544.493121.1589
30.5708-0.2664-0.54450.8209-0.27120.9029-0.14650.0341-0.0175-0.1845-0.05880.15330.3107-0.0367-0.00140.62510.0168-0.02520.51290.05980.5573-54.00124.614516.3432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 312 )

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