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- PDB-2f00: Escherichia coli MurC -

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Basic information

Entry
Database: PDB / ID: 2f00
TitleEscherichia coli MurC
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / amide bond ligase / ATPase / bacterial cell wall
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / 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 ...UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / 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
UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsDeva, T. / Baker, E.N. / Squire, C.J. / Smith, C.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of Escherichia coliUDP-N-acetylmuramoyl:L-alanine ligase (MurC).
Authors: Deva, T. / Baker, E.N. / Squire, C.J. / Smith, C.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Purification, crystallization and preliminary X-ray analysis of Escherichia coli UDP-N-acetylmuramoyl:L-alanine ligase (MurC).
Authors: Deva, T. / Pryor, K.D. / Leiting, B. / Baker, E.N. / Smith, C.A.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-N-acetylmuramate--L-alanine ligase
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8334
Polymers108,7842
Non-polymers492
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.926, 93.134, 176.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer

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Components

#1: Protein UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 54392.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: murC / Production host: Escherichia coli (E. coli)
References: UniProt: P17952, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 12-16% mPEG5000, 0.2 M Bis-Tris Propane pH 8.3, 10 mM MgCl2, 50 mM beta-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9790, 0.9792, 0.8377
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2003
RadiationMonochromator: single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.83771
ReflectionResolution: 2.5→88 Å / Num. obs: 42732 / % possible obs: 99.3 % / Redundancy: 20 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 20.8
Reflection shellResolution: 2.5→2.6 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→88 Å / σ(F): 0 / Details: CNS 1.1 was also used for refinement.
RfactorNum. reflectionSelection details
Rfree0.26 2137 randomly selected 5%
Rwork0.217 --
all0.219 42671 -
obs-42671 -
Refinement stepCycle: LAST / Resolution: 2.5→88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 0 12 368 7582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.08

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