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- PDB-1e0d: UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase -

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Basic information

Entry
Database: PDB / ID: 1e0d
TitleUDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase
ComponentsUDP-N-ACETYLMURAMOYLALANINE--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 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 domain / Mur-like, catalytic 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 ...UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal domain / Mur-like, catalytic 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 / 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
UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFanchon, E. / Bertrand, J. / Chantalat, L. / Dideberg, O.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: "Open" Structures of Murd: Domain Movements and Structural Similarities with Folylpolyglutamate Synthetase.
Authors: Bertrand, J. / Fanchon, E. / Martin, L. / Chantalat, L. / Auger, G. / Blanot, D. / Van Heijenoort, J. / Dideberg, O.
History
DepositionMar 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jun 13, 2018Group: Advisory / Data collection / Structure summary
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct
Item: _diffrn_source.pdbx_synchrotron_beamline / _struct.title
Revision 1.3Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _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

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)46,9852
Polymers46,8891
Non-polymers961
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.160, 69.160, 196.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE / MURD


Mass: 46889.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: JM83 (PMLD58)URCE / Gene: MURD GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 (PMLD58)URCE
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.8 mg/mlprotein1drop
21 mM1dropNaN3
31 mMdithiothreitol1drop
420 mMHEPES1drop
51.5-1.7 Mammonium sulfate1reservoir
6100 mMMES1reservoir
75 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: D2AM / Wavelength: 0.9801
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19294 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.8 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.21 / % possible all: 99.9
Reflection
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.212

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Processing

Software
NameVersionClassification
CNS0.4refinement
XDSdata reduction
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2 DOMAINS FROM 1UAG

1uag


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1911015.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY. RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON ...Details: RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY. RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 781 4.9 %RANDOM
Rwork0.213 ---
obs0.213 15985 82 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.2219 Å2 / ksol: 0.365383 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å20 Å20 Å2
2--3.89 Å20 Å2
3----7.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 5 229 3449
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 93 5 %
Rwork0.246 1765 -
obs--58.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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