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- PDB-2am1: sp protein ligand 1 -

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Basic information

Entry
Database: PDB / ID: 2am1
Titlesp protein ligand 1
ComponentsUDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase, MurF protein
KeywordsLIGASE
Function / homology
Function and homology information


UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 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 ...UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1LG / : / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsLongenecker, K.L. / Stamper, G.F. / Hajduk, P.J. / Fry, E.H. / Jakob, C.G. / Harlan, J.E. / Edalji, R. / Bartley, D.M. / Walter, K.A. / Solomon, L.R.
CitationJournal: Protein Sci. / Year: 2005
Title: Structure of MurF from Streptococcus pneumoniae co-crystallized with a small molecule inhibitor exhibits interdomain closure
Authors: Longenecker, K.L. / Stamper, G.F. / Hajduk, P.J. / Fry, E.H. / Jakob, C.G. / Harlan, J.E. / Edalji, R. / Bartley, D.M. / Walter, K.A. / Solomon, L.R. / Holzman, T.F. / Gu, Y.G. / Lerner, C.G. ...Authors: Longenecker, K.L. / Stamper, G.F. / Hajduk, P.J. / Fry, E.H. / Jakob, C.G. / Harlan, J.E. / Edalji, R. / Bartley, D.M. / Walter, K.A. / Solomon, L.R. / Holzman, T.F. / Gu, Y.G. / Lerner, C.G. / Beutel, B.A. / Stoll, V.S.
History
DepositionAug 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase, MurF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3393
Polymers50,7471
Non-polymers5932
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.271, 116.271, 161.389
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase, MurF protein / sp protein


Mass: 50746.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: murF / Production host: Escherichia coli (E. coli)
References: GenBank: 15459176, UniProt: Q8DNV6*PLUS, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase
#2: Chemical ChemComp-1LG / 2,4-DICHLORO-N-(3-CYANO-4,5,6,7-TETRAHYDRO-BENZOTHIOPHEN-2YL)-5-(MORPHOLINE-4-SULFONYL)-BENZAMIDE


Mass: 500.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19Cl2N3O4S2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.36 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 22837 / % possible obs: 99.3 % / Rmerge(I) obs: 0.072 / Χ2: 2.082
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2.5-2.5998.50.37922070.8371
2.59-2.691000.31522540.8611
2.69-2.821000.22522380.961
2.82-2.961000.167226411
2.96-3.151000.11522681.1571
3.15-3.391000.08522601.4171
3.39-3.731000.06922941.9641
3.73-4.2799.50.05822952.3761
4.27-5.3898.90.05323303.241
5.38-3096.70.05624276.4761

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1166 5.1 %random
Rwork0.238 ---
all0.238 22888 --
obs0.238 22739 99.3 %-
Displacement parametersBiso mean: 51.495 Å2
Baniso -1Baniso -2Baniso -3
1-3.462 Å2-0.072 Å20 Å2
2--3.462 Å20 Å2
3----6.924 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3499 0 37 139 3675
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2lig.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4gol.par

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