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- PDB-1ufv: Crystal Structure Of Pantothenate Synthetase From Thermus Thermop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ufv | ||||||
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Title | Crystal Structure Of Pantothenate Synthetase From Thermus Thermophilus HB8 | ||||||
![]() | Pantoate-beta-alanine ligase | ||||||
![]() | LIGASE / Structural Genomics / Dimer / Domains / Rossmann Fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bagautdinov, B. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal Structure Of Pantothenate Synthetase From Thermus Thermophilus HB8 Authors: Bagautdinov, B. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.8 KB | Display | ![]() |
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PDB format | ![]() | 103 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1v8fC ![]() 1n2eS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The bilogical assembly is a dimer |
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Components
#1: Protein | Mass: 30939.727 Da / Num. of mol.: 2 / Mutation: V48A Source method: isolated from a genetically manipulated source Details: Mutation of VAL 48 to ALA / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P83701, UniProt: Q5SHF5*PLUS, pantoate-beta-alanine ligase (AMP-forming) #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8 Details: PEG4000, TRIS, lithium cloride, pH 8, MICROBATCH, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 2, 2002 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. all: 602701 / Num. obs: 602601 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 7.5 / Num. unique all: 3898 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N2E Resolution: 2.05→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Refinement performed using anomalous f', f'' library file for Se, Cl at 1 Angstrom
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Displacement parameters | Biso mean: 39.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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