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- PDB-8v8x: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate... -

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Basic information

Entry
Database: PDB / ID: 8v8x
TitleCrystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (Orthorhombic P form2)
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
GLYCINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 (Orthorhombic P form2)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9812
Polymers47,9061
Non-polymers751
Water91951
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)57.796, 63.192, 119.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus H4: 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 DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine ...Details: Morpheus H4: 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 DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Inhibitor added but not bound. plate 13512 well H4 drop 2. Puck: PSL-1715, 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: 2.3→43.51 Å / Num. obs: 20187 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.064 / Rrim(I) all: 0.167 / Χ2: 1 / Net I/σ(I): 8.2 / Num. measured all: 134921
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.983 / Num. measured all: 13766 / Num. unique obs: 1952 / CC1/2: 0.777 / Rpim(I) all: 0.396 / Rrim(I) all: 1.061 / Χ2: 1.04 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5162: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.65 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 969 4.82 %
Rwork0.2133 --
obs0.2153 20112 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 5 51 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023210
X-RAY DIFFRACTIONf_angle_d0.4754355
X-RAY DIFFRACTIONf_dihedral_angle_d13.8461158
X-RAY DIFFRACTIONf_chiral_restr0.041514
X-RAY DIFFRACTIONf_plane_restr0.004572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.29271370.25692698X-RAY DIFFRACTION100
2.42-2.570.32431560.25752653X-RAY DIFFRACTION100
2.57-2.770.33841300.25972716X-RAY DIFFRACTION100
2.77-3.050.30521350.25562704X-RAY DIFFRACTION100
3.05-3.490.2741480.22922710X-RAY DIFFRACTION100
3.49-4.40.22511310.18362767X-RAY DIFFRACTION100
4.4-42.650.20611320.18422895X-RAY DIFFRACTION99
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)
11.08040.4291-0.19473.16171.16813.1637-0.01280.1022-0.013-0.2332-0.10570.0219-0.2185-0.25410.11060.27160.0814-0.02320.3913-0.00360.2616-9.684-24.336-37.131
21.35370.10340.4240.75930.02112.6270.0070.0705-0.0956-0.01390.0043-0.09320.0830.1051-0.01040.21450.01360.01790.2108-0.00060.3314-0.103-20.953-9.028
31.32441.0894-0.61881.8795-1.38123.0175-0.26860.1286-0.1195-0.43840.30460.24481.3052-0.7132-0.01410.7501-0.17680.01940.49390.01230.455-24.544-38.91-7.035
422226.73132-1.025-2.72277.1722.8118-0.25850.9285-4.30723.60881.27050.45820.0225-0.18960.7464-0.23950.5981-20.249-21.264-4.722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:101 )A1 - 101
2X-RAY DIFFRACTION2( CHAIN A AND RESID 102:281 )A102 - 281
3X-RAY DIFFRACTION3( CHAIN A AND RESID 282:438 )A282 - 438
4X-RAY DIFFRACTION4( CHAIN A AND RESID 501:501 )A501

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