+Open data
-Basic information
Entry | Database: PDB / ID: 3uag | ||||||
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Title | UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE | ||||||
Components | PROTEIN (UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE) | ||||||
Keywords | LIGASE / 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.77 Å | ||||||
Authors | Bertrand, J.A. / Auger, G. / Martin, L. / Fanchon, E. / Blanot, D. / Le Beller, D. / Van Heijenoort, J. / Dideberg, O. | ||||||
Citation | 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. #1: Journal: Protein Expr.Purif. / Year: 1998 Title: Large-scale preparation, purification, and crystallization of UDP-N-acetylmuramoyl-L-alanine: D-glutamate ligase from Escherichia coli. Authors: Auger, G. / Martin, L. / Bertrand, J. / Ferrari, P. / Fanchon, E. / Vaganay, S. / Petillot, Y. / van Heijenoort, J. / Blanot, D. / Dideberg, O. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uag.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uag.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 3uag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/3uag ftp://data.pdbj.org/pub/pdb/validation_reports/ua/3uag | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46932.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: UMA, ADP & MANGANESE BOUND, PH 7.2 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM83 (PMLD58) / 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 |
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-Non-polymers , 5 types, 363 molecules
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-UMA / |
#4: Chemical | ChemComp-ADP / |
#5: Chemical | ChemComp-EPE / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | RESIDUE 198 IS A MODIFIED LYSINE WHICH IS CARBAMYLATED AT THE ZETA-AMINO GROUP. THE CARBAMYLATED ...RESIDUE 198 IS A MODIFIED LYSINE WHICH IS CARBAMYLAT | ||
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Nonpolymer details | RESIDUE 198 IS A MODIFIED LYSINE WHICH IS CARBAMYLATSequence details | KCX 198, MODIFIED LYSINE RESIDUE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.62 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusionDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.881 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.881 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→65.9 Å / Num. obs: 54268 / % possible obs: 99.2 % / Redundancy: 4.6 % / Rsym value: 0.066 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 8.6 / Rsym value: 0.204 / % possible all: 98.7 |
Reflection | *PLUS Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.204 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.77→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 16.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.85 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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