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- PDB-1lh0: Crystal Structure of Salmonella typhimurium OMP Synthase in Compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lh0 | ||||||
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Title | Crystal Structure of Salmonella typhimurium OMP Synthase in Complex with MGPRPP and Orotate | ||||||
![]() | OMP synthase | ||||||
![]() | TRANSFERASE / loop closure / monomer closure / orotate phosphoribosyltransferase | ||||||
Function / homology | ![]() pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Panneerselvam, K. / Shi, W. / Grubmeyer, C. / Almo, S.C. | ||||||
![]() | ![]() Title: Structure of Salmonella typhimurium OMP Synthase in a Complete Substrate Complex. Authors: Grubmeyer, C. / Hansen, M.R. / Fedorov, A.A. / Almo, S.C. #1: ![]() Title: Crystal structure of orotate phosphoribosyltransferase Authors: Scapin, G. / Grubmeyer, C. / Sacchettini, J.C. #2: ![]() Title: The crystal structure of the orotate phosphoribosyltransferase complexed with orotate and alpha-D-5-phosphoribosyl-1-pyrophosphate Authors: Scapin, G. / Ozturk, D.H. / Grubmeyer, C. / Sacchettini, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.5 KB | Display | ![]() |
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PDB format | ![]() | 77.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.9 KB | Display | ![]() |
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Full document | ![]() | 471 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oroS ![]() 1i2i S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer |
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Components
#1: Protein | Mass: 23591.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P08870, orotate phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Sugar | ChemComp-PRP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: tri-sodium citrate, PRPP, orotate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 2, 2000 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 29408 / Num. obs: 29408 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.1 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ORO Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 48.9 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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