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- PDB-1eeh: UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE -

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Basic information

Entry
Database: PDB / ID: 1eeh
TitleUDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
ComponentsUDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / MURD / ADP-FORMING ENZYME
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 cycle / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Mur ligase MurD-like, N-terminal domain / UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain ...Mur ligase MurD-like, N-terminal domain / UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBertrand, J.A. / Fanchon, E. / Martin, L. / Chantalat, L. / Auger, G. / Blanot, D. / van Heijenoort, J. / Dideberg, O.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: "Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase.
Authors: Bertrand, J.A. / Fanchon, E. / Martin, L. / Chantalat, L. / Auger, G. / Blanot, D. / van Heijenoort, J. / Dideberg, O.
#1: Journal: Embo J. / Year: 1997
Title: Crystal Structure of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli
Authors: Bertrand, J.A. / Auger, G. / Fanchon, E. / Martin, L. / Blanot, D. / van Heijenoort, J. / Dideberg, O.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Determination of the MurD mechanism through crystallographic analysis of enzyme complexes
Authors: Bertrand, J.A. / Auger, G. / Martin, L. / Fanchon, E. / Blanot, D. / Le Beller, D. / van Heijenoort, J. / Dideberg, O.
History
DepositionJan 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6402
Polymers46,8891
Non-polymers7501
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.840, 63.280, 114.910
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-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE


Mass: 46889.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PROTEIN SOLUTION: 9.8 mg/ml MURD, 1 mM UMA, 1 mM Sodium Azide, 1 mM DTT, 20 mM HEPES pH 7.5 RESEVOIR: 5-9 % PEG 3350 Monodisperse, 100 mM sodium Acetate pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.8 mg/mlMurD1drop
21 mMUMA1drop
31 mM1dropNaN3
41 mMdithiothreitol1drop
520 mMHEPES1drop
65-9 %(w/v)PEG3350 monodisperse1reservoir
7100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.073
DetectorType: XRII-CCD / Detector: CCD / Date: Sep 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
ReflectionResolution: 1.878→13.392 Å / Num. all: 31255 / Num. obs: 31255 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 11.4 Å2 / Rsym value: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 1.88→1.94 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1675 / Rsym value: 0.279 / % possible all: 49.1
Reflection
*PLUS
Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Lowest resolution: 1.93 Å / % possible obs: 49.1 % / Rmerge(I) obs: 0.164

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 1.9→13 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Electron density was weak for residues 111-116 and residues 220-226. In addition, residues 240-245 were not visible in the electron density and their coordinates are not included in this entry.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2034 7.2 %RANDOM
Rwork0.219 ---
all0.226 28445 --
obs0.226 26411 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1361 Å2 / ksol: 0.458667 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å20 Å2
2---4.17 Å20 Å2
3---1.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 49 186 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.512.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 274 8 %
Rwork0.224 3131 -
obs--60.3 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 13 Å / σ(F): 0 / % reflection Rfree: 7.2 % / Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.286 / % reflection Rfree: 8 % / Rfactor Rwork: 0.224

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