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

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Basic information

Entry
Database: PDB / ID: 1uag
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 / MAD, MIR / Resolution: 1.95 Å
AuthorsBertrand, J. / Fanchon, E. / Dideberg, O.
CitationJournal: 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.
History
DepositionMar 13, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)47,8754
Polymers46,9321
Non-polymers9433
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.428, 65.428, 134.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein UDP-N-ACETYLMURAMOYL-L-ALANINE/:D-GLUTAMATE LIGASE / MURD


Mass: 46932.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UDP-N-ACETYLMURAMOYL-L-ALANINE BOUND, PH 7.2 / Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: JM83 / Gene: MURD GENE / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 (PMLD58)
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE 198 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. THE CARBAMYLATED ...RESIDUE 198 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. THE CARBAMYLATED RESIDUE IS PRESENTED AS HET GROUP KCX.

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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: 3 Å3/Da / Density % sol: 59.86 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 15 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Auger, G., (1998) Protein Expr. Purif., 13, 23.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.8 mg/mlprotein1drop
21 mMUMA1drop
31 mM1dropNaN3
41 mMdithiothreitol1drop
520 mMsodium HEPES1drop
61.6-1.8 Mammonium sulfate1reservoir
7100 mMsodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.0722
DetectorDetector: CDD / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.89→36.97 Å / Num. obs: 41111 / % possible obs: 78.7 % / Redundancy: 3.5 % / Rsym value: 0.065 / Net I/σ(I): 8.7
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.03 / Rsym value: 0.259 / % possible all: 29.5
Reflection
*PLUS
% possible obs: 94.7 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 79.7 % / Rmerge(I) obs: 0.259

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Processing

Software
NameVersionClassification
XDSdata scaling
MADSYSphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD, MIR / Resolution: 1.95→8 Å
RfactorNum. reflection% reflection
Rfree0.235 -4.35 %
Rwork0.19 --
obs0.19 34834 88.36 %
Displacement parametersBiso mean: 13.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 59 294 3575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.95→2.04 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.269 2.81 %
Rwork0.228 -
obs-58.95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_deg2.27

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