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- PDB-8vw0: Crystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate... -

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Basic information

Entry
Database: PDB / ID: 8vw0
TitleCrystal Structure of Apo UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli (AMP 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 MONOPHOSPHATE / 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 (AMP 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)48,75811
Polymers47,9491
Non-polymers80810
Water4,756264
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)58.136, 68.824, 100.576
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, 274 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / 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.: 264 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
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 AMP. plate 13768 well E4 drop 1 or 2. Puck: PSL-1103, 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→44.41 Å / Num. obs: 45018 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.026 / Rrim(I) all: 0.097 / Χ2: 1.02 / Net I/σ(I): 16.2 / Num. measured all: 599313
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 98.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 1.745 / Num. measured all: 32489 / Num. unique obs: 2349 / CC1/2: 0.759 / Rpim(I) all: 0.482 / Rrim(I) all: 1.811 / Χ2: 1.06 / Net I/σ(I) obs: 1.7

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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→40.63 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 2209 4.92 %
Rwork0.1607 --
obs0.1624 44921 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 42 264 3572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083362
X-RAY DIFFRACTIONf_angle_d0.924572
X-RAY DIFFRACTIONf_dihedral_angle_d13.0461217
X-RAY DIFFRACTIONf_chiral_restr0.053535
X-RAY DIFFRACTIONf_plane_restr0.007597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.29051450.27662600X-RAY DIFFRACTION99
1.74-1.780.28961300.24172603X-RAY DIFFRACTION99
1.78-1.820.26221430.22292632X-RAY DIFFRACTION99
1.82-1.870.24181240.19532630X-RAY DIFFRACTION99
1.87-1.930.22051190.18172627X-RAY DIFFRACTION99
1.93-1.990.23281350.1932653X-RAY DIFFRACTION99
1.99-2.060.21261730.17672593X-RAY DIFFRACTION100
2.06-2.140.19541330.162685X-RAY DIFFRACTION100
2.14-2.240.20681400.15592644X-RAY DIFFRACTION100
2.24-2.360.20561480.14782635X-RAY DIFFRACTION100
2.36-2.50.20181310.15282699X-RAY DIFFRACTION100
2.51-2.70.18071350.15842678X-RAY DIFFRACTION100
2.7-2.970.22791430.1592686X-RAY DIFFRACTION100
2.97-3.40.16681330.15512728X-RAY DIFFRACTION100
3.4-4.280.19581320.13472744X-RAY DIFFRACTION100
4.28-40.630.17081450.16082875X-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)
12.9180.5260.82971.8003-0.00424.12560.0044-0.2127-0.05890.17520.018-0.02630.0314-0.04960.00340.23590.00850.00040.14870.01980.1526-5.0525-14.8763-3.3352
21.0973-0.1902-0.15971.90510.31652.43850.00030.0458-0.04140.0413-0.0003-0.0870.10210.14140.01990.1344-0.0072-0.02610.1153-0.00290.1775-0.0786-23.1048-31.1172
33.4581-0.2720.91292.11930.22752.58210.02510.0064-0.30570.04950.146-0.01730.10440.0956-0.16910.1456-0.0068-0.00420.30190.0140.189726.0212-17.975-29.5564
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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