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- PDB-8vw1: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate... -

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Basic information

Entry
Database: PDB / ID: 8vw1
TitleCrystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (ADP bound)
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
ADENOSINE-5'-DIPHOSPHATE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 (ADP bound)
Authors: Seibold, S. / Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: 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)48,76610
Polymers47,9491
Non-polymers8179
Water3,963220
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)58.470, 69.235, 100.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase / D-glutamic acid-adding enzyme / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase


Mass: 47949.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murD, b0088, JW0086 / Plasmid: EscoA.17938.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

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Non-polymers , 6 types, 229 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: 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
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, 2% (v/v) DMSO. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. 4 hour ...Details: Morpheus A8: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM HEPES/MOPS, pH 7.5, 30 mM MgCl2 and 30 mM CaCl2, 2% (v/v) DMSO. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. 4 hour soak in 5 mM ADP. plate 13768 well E4 drop 1 or 2. Puck: PSL-1105, 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: 0.9785 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.7→44.67 Å / Num. obs: 45584 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Χ2: 1.04 / Net I/σ(I): 15 / Num. measured all: 600089
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.4 % / Redundancy: 13.7 % / Rmerge(I) obs: 1.874 / Num. measured all: 32440 / Num. unique obs: 2371 / CC1/2: 0.723 / Rpim(I) all: 0.519 / Rrim(I) all: 1.945 / Χ2: 1.07 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21_5219: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.82 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 2238 4.92 %
Rwork0.1628 --
obs0.1644 45480 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 45 220 3517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093356
X-RAY DIFFRACTIONf_angle_d1.0474568
X-RAY DIFFRACTIONf_dihedral_angle_d13.9761208
X-RAY DIFFRACTIONf_chiral_restr0.059536
X-RAY DIFFRACTIONf_plane_restr0.008595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.33121340.28032662X-RAY DIFFRACTION99
1.74-1.780.24091450.24422645X-RAY DIFFRACTION99
1.78-1.820.27711490.22092656X-RAY DIFFRACTION100
1.82-1.870.21931220.19772644X-RAY DIFFRACTION100
1.87-1.930.23221210.18612700X-RAY DIFFRACTION100
1.93-1.990.21491350.19122661X-RAY DIFFRACTION100
1.99-2.060.20381740.16692646X-RAY DIFFRACTION100
2.06-2.140.19371410.15452681X-RAY DIFFRACTION100
2.14-2.240.18591370.14932683X-RAY DIFFRACTION100
2.24-2.360.18551480.14592691X-RAY DIFFRACTION100
2.36-2.50.19451380.15142704X-RAY DIFFRACTION100
2.51-2.70.18161330.16462708X-RAY DIFFRACTION100
2.7-2.970.22641470.16282720X-RAY DIFFRACTION100
2.97-3.40.19791360.16322750X-RAY DIFFRACTION100
3.4-4.280.1871300.1392785X-RAY DIFFRACTION100
4.28-40.820.17321480.1652906X-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)
12.70590.31330.96452.108-0.08564.4408-0.0005-0.1311-0.06760.14760.0176-0.0465-0.0073-0.0145-0.00930.2410.00610.00770.19080.01490.1942-4.9979-14.9245-3.3237
21.1281-0.2581-0.23141.69770.34622.88040.00880.0239-0.04090.0245-0.0172-0.04210.10440.09890.01620.1524-0.0104-0.02890.1376-0.00010.19580.0083-23.3797-31.0507
33.21370.23960.40971.97320.17362.46850.03130.1544-0.24240.03340.0883-0.09020.13540.3246-0.11060.16030.0072-0.00410.3075-0.0130.18726.29-17.9645-29.5461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 296 )
3X-RAY DIFFRACTION3chain 'A' and (resid 297 through 440 )

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