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Open data
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Basic information
Entry | Database: PDB / ID: 1zis | ||||||
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Title | Recombinant Lumazine synthase (hexagonal form) | ||||||
![]() | 6,7-dimethyl-8-ribityllumazine synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lopez-Jaramillo, F.J. | ||||||
![]() | ![]() Title: Crystal structure of recombinant Lumazine synthase (hexagonal form) Authors: Lopez-Jaramillo, F.J. #1: ![]() Title: Studies on the Lumazine Synthase/Riboflavin Synthase Complex of Bacillus subtilis: Crystal Structure Analysis of Reconstituted, Icosahedral b-subunit Capsids with Bound Substrate Analogue ...Title: Studies on the Lumazine Synthase/Riboflavin Synthase Complex of Bacillus subtilis: Crystal Structure Analysis of Reconstituted, Icosahedral b-subunit Capsids with Bound Substrate Analogue Inhibitor at 2.4 A Resolution Authors: Ritsert, K. / Huber, R. / Turk, D. / Ladenstein, R. / Scmidt-Base, K. / Bacher, A. #2: ![]() Title: Heavy Riboflavin Synthase from Bacillus subtilis: Crystal Structure Analysis of the Icosahedral b60 Capsid at 3.3 A Resolution Authors: Ladenstein, R. / Schneider, M. / Huber, R. / Bartunik, H.-D. / Wilson, K. / Schott, K. / Bacher, A. #3: ![]() Title: The Lumazine Synthase-Riboflavin Synthase Complex of Bacillus subtilis. Crystallization of Reconstituted Icosahedral b-subunit Capsids Authors: Schott, K. / Ladenstein, R. / Konig, A. / Bacher, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.6 KB | Display | ![]() |
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PDB format | ![]() | 224.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.5 MB | Display | |
Data in XML | ![]() | 66.8 KB | Display | |
Data in CIF | ![]() | 79.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rvvS 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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1 | ![]()
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2 | ![]()
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3 | x 6 ![]()
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4 | x 6 ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16302.567 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P11998, 6,7-dimethyl-8-ribityllumazine synthase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-INI / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.7 Details: Phosphate buffer, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 22, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.6 Å / Num. obs: 40931 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 44.616 Å2 / Limit h max: 45 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 102 / Limit l min: 0 / Observed criterion F max: 7253072.27 / Observed criterion F min: 83.39 / Rmerge(I) obs: 0.085 / Rsym value: 0.073 / Net I/σ(I): 17.59 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.38 / Num. unique all: 3377 / Rsym value: 0.15 / % possible all: 77.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pentamer from 1RVV Resolution: 2.9→10 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 24.9564 Å2 / ksol: 0.327727 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 194.39 Å2 / Biso mean: 44.29 Å2 / Biso min: 5.71 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Xplor file |
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