+Open data
-Basic information
Entry | Database: PDB / ID: 1g95 | ||||||
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Title | CRYSTAL STRUCTURE OF S.PNEUMONIAE GLMU, APO FORM | ||||||
Components | N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GlmU / Acetyltransferase / uridyltransferase pyrophosphorylase / left-handed beta-sheet helix / trimer | ||||||
Function / homology | Function and homology information glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.33 Å | ||||||
Authors | Kostrewa, D. / D'Arcy, A. / Kamber, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structures of Streptococcus pneumoniae N-acetylglucosamine-1-phosphate uridyltransferase, GlmU, in apo form at 2.33 A resolution and in complex with UDP-N-acetylglucosamine and Mg(2+) at 1.96 A resolution. Authors: Kostrewa, D. / D'Arcy, A. / Takacs, B. / Kamber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g95.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g95.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g95_validation.pdf.gz | 412.5 KB | Display | wwPDB validaton report |
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Full document | 1g95_full_validation.pdf.gz | 418.8 KB | Display | |
Data in XML | 1g95_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1g95_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/1g95 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/1g95 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -Y+1, X-Y, Z and -X+Y+1, -X+1, Z |
-Components
#1: Protein | Mass: 49398.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q97R46, UDP-N-acetylglucosamine diphosphorylase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M BIS/TRIS, 0.2 M ammonium sulfate, 25 % PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873 / Wavelength: 0.873 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1998 / Details: Mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→30 Å / Num. all: 37195 / Num. obs: 20586 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.061 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2007 / Rsym value: 0.188 / % possible all: 95.7 |
Reflection | *PLUS Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 95.7 % / Rmerge(I) obs: 0.188 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.33→30 Å / Isotropic thermal model: isotropic / Cross valid method: FREE-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT CORRECTION WITH ELECTRON DENSITY = 0.26 E/A**3, B-FACTOR = 23.5 A**2. THE FOLLOWING AMINO ACID RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS: 188-193, 453-459. THE ...Details: BULK SOLVENT CORRECTION WITH ELECTRON DENSITY = 0.26 E/A**3, B-FACTOR = 23.5 A**2. THE FOLLOWING AMINO ACID RESIDUES WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS: 188-193, 453-459. THE ELECTRON DENSITY MAPS OF THE FOLLOWING AMINO ACID RESIDUES WERE OF RELATIVELY POOR QUALITY: 2, 10-12, 51-94, 145-149, 154-164, 179-187, 194-197, 439-441, 447-452. THE WATER MOLECULES ARE ORDERED WITH ASCENDING B-FACTORS.
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Solvent computation | Solvent model: bulk solvent mask / Bsol: 23.5 Å2 / ksol: 0.26 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.33→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.41 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.23 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.1 Å2 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.35 / % reflection Rfree: 5 % / Rfactor Rwork: 0.306 |