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- PDB-9bn8: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -

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Basic information

Entry
Database: PDB / ID: 9bn8
TitleCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE/LIGASE INHIBITOR / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal 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
: / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
Authors: Liu, L. / Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionMay 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,10615
Polymers47,9061
Non-polymers2,20014
Water9,080504
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.488, 65.488, 134.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase


Mass: 47906.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murD / Plasmid: EscoA.17938.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14900

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Non-polymers , 5 types, 518 molecules

#2: Chemical ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE


Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O20P2
#3: Chemical ChemComp-A1AQS / N-(4-{[(4S)-3-amino[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl}phenyl)acetamide


Mass: 300.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N6OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the ...Details: 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the same solution for another 2h. plate Liu-Lim-116 A2. Puck: PSL-0401, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19

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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: Apr 13, 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: 1.35→67.38 Å / Num. obs: 124023 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.072 / Χ2: 0.99 / Net I/σ(I): 17.7 / Num. measured all: 1676743
Reflection shellResolution: 1.35→1.39 Å / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 1.317 / Num. measured all: 91897 / Num. unique obs: 9171 / CC1/2: 0.682 / Rpim(I) all: 0.435 / Rrim(I) all: 1.388 / Χ2: 1.01 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(dev_5318: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→58.9 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 6027 4.86 %
Rwork0.1327 --
obs0.1339 123930 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 131 504 3895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073577
X-RAY DIFFRACTIONf_angle_d0.9194895
X-RAY DIFFRACTIONf_dihedral_angle_d12.3791285
X-RAY DIFFRACTIONf_chiral_restr0.079560
X-RAY DIFFRACTIONf_plane_restr0.011633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.24012470.21673946X-RAY DIFFRACTION100
1.37-1.380.22772280.20453856X-RAY DIFFRACTION100
1.38-1.40.22251490.19383962X-RAY DIFFRACTION100
1.4-1.420.21251950.18313932X-RAY DIFFRACTION100
1.42-1.430.24841910.19713911X-RAY DIFFRACTION100
1.43-1.450.22482090.18633943X-RAY DIFFRACTION100
1.45-1.480.19281990.16643897X-RAY DIFFRACTION100
1.48-1.50.21191690.14883968X-RAY DIFFRACTION100
1.5-1.520.17262000.13323918X-RAY DIFFRACTION100
1.52-1.550.1461940.12223949X-RAY DIFFRACTION100
1.55-1.570.1392230.11283873X-RAY DIFFRACTION100
1.57-1.60.14111860.10863945X-RAY DIFFRACTION100
1.6-1.630.14041850.1123951X-RAY DIFFRACTION100
1.63-1.660.15551630.1153932X-RAY DIFFRACTION100
1.66-1.70.1552080.12043921X-RAY DIFFRACTION100
1.7-1.740.13652010.12633946X-RAY DIFFRACTION100
1.74-1.780.15392170.13183880X-RAY DIFFRACTION100
1.78-1.830.16661890.14133946X-RAY DIFFRACTION100
1.83-1.890.14711880.13013950X-RAY DIFFRACTION100
1.89-1.950.14721930.12123927X-RAY DIFFRACTION100
1.95-2.020.14112350.12033885X-RAY DIFFRACTION100
2.02-2.10.14932150.11513947X-RAY DIFFRACTION100
2.1-2.190.14782150.11663903X-RAY DIFFRACTION100
2.19-2.310.1412190.11873910X-RAY DIFFRACTION100
2.31-2.450.13561750.11533964X-RAY DIFFRACTION100
2.45-2.640.16082120.12623935X-RAY DIFFRACTION100
2.64-2.910.15741860.14033945X-RAY DIFFRACTION100
2.91-3.330.17032280.14223923X-RAY DIFFRACTION100
3.33-4.190.1392060.12573961X-RAY DIFFRACTION100
4.2-58.90.1692020.14633977X-RAY DIFFRACTION100

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