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- PDB-8v8w: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate... -

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Basic information

Entry
Database: PDB / ID: 8v8w
TitleCrystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Tetragonal P form)
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD
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
ACETATE ION / OXAMIC ACID / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Tetragonal P form)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionDec 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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)48,3586
Polymers47,9061
Non-polymers4515
Water4,125229
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)67.801, 67.801, 200.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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, 234 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus G4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM ...Details: Morpheus G4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Inhibitor added but not bound. plate 13512 well G4 drop 1. Puck: PSL-1712, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 8, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→47.94 Å / Num. obs: 57294 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.026 / Rrim(I) all: 0.092 / Χ2: 0.98 / Net I/σ(I): 13.8 / Num. measured all: 740487
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.582 / Num. measured all: 37493 / Num. unique obs: 2762 / CC1/2: 0.808 / Rpim(I) all: 0.444 / Rrim(I) all: 1.644 / Χ2: 0.97 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5162: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2876 5.03 %
Rwork0.1786 --
obs0.1796 57142 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 29 229 3469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093336
X-RAY DIFFRACTIONf_angle_d0.9784539
X-RAY DIFFRACTIONf_dihedral_angle_d14.1721213
X-RAY DIFFRACTIONf_chiral_restr0.058530
X-RAY DIFFRACTIONf_plane_restr0.008601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.39091190.34152541X-RAY DIFFRACTION100
1.68-1.710.31241540.30792519X-RAY DIFFRACTION100
1.71-1.740.32891300.27712548X-RAY DIFFRACTION100
1.74-1.770.2541510.25962490X-RAY DIFFRACTION100
1.77-1.810.27371360.242543X-RAY DIFFRACTION100
1.81-1.850.21571230.21692556X-RAY DIFFRACTION100
1.85-1.890.23891300.1992547X-RAY DIFFRACTION100
1.89-1.940.21521440.18672535X-RAY DIFFRACTION100
1.94-1.990.23941290.18582554X-RAY DIFFRACTION100
1.99-2.050.24321180.19482574X-RAY DIFFRACTION100
2.05-2.110.22971580.20472544X-RAY DIFFRACTION100
2.11-2.190.21081270.17652582X-RAY DIFFRACTION100
2.19-2.280.18561440.16492543X-RAY DIFFRACTION100
2.28-2.380.20771230.16972576X-RAY DIFFRACTION100
2.38-2.510.17431170.1742628X-RAY DIFFRACTION100
2.51-2.660.22291250.17832592X-RAY DIFFRACTION100
2.66-2.870.20281430.18612600X-RAY DIFFRACTION100
2.87-3.160.18761520.18192613X-RAY DIFFRACTION100
3.16-3.610.18951470.16992642X-RAY DIFFRACTION100
3.61-4.550.17151520.14642686X-RAY DIFFRACTION100
4.55-47.540.17441540.17342853X-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)
13.0629-1.0374-0.42122.55070.01513.8655-0.021-0.3189-0.11970.2161-0.01660.01460.0498-0.30370.04750.1457-0.0458-0.02090.28350.06640.18430.2253-28.029846.6642
20.78340.2299-0.0711.1443-1.39223.45160.0784-0.2281-0.10330.0756-0.1471-0.1116-0.13570.33110.04190.1563-0.0004-0.01760.2497-0.00040.205811.2495-20.809928.063
34.42010.746-0.13854.1314-0.42863.70490.1080.17030.2869-0.0661-0.0822-0.058-0.33670.1403-0.01920.16360.01240.00270.16590.00130.126910.7838-9.03748.3677
42.48880.0152-0.11174.33770.18874.01550.0658-0.27030.50660.4689-0.04020.0535-0.49130.21010.00590.2843-0.02790.00890.2073-0.04610.3272-0.80210.258421.6493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 226 )
3X-RAY DIFFRACTION3chain 'A' and (resid 227 through 295 )
4X-RAY DIFFRACTION4chain 'A' and (resid 296 through 438 )

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