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- PDB-1bu5: X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBORO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bu5 | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE DESULFOVIBRIO VULGARIS (HILDENBOROUGH) APOFLAVODOXIN-RIBOFLAVIN COMPLEX | ||||||
![]() | PROTEIN (FLAVODOXIN) | ||||||
![]() | ELECTRON TRANSPORT / FLAVOPROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walsh, M.A. / Mccarthy, A. / O'Farrell, P.A. / Mccardle, P. / Cunningham, P.D. / Mayhew, S.G. / Higgins, T.M. | ||||||
![]() | ![]() Title: X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex. Authors: Walsh, M.A. / McCarthy, A. / O'Farrell, P.A. / McArdle, P. / Cunningham, P.D. / Mayhew, S.G. / Higgins, T.M. #1: ![]() Title: Comparison of the Crystal Structures of a Flavodoxin in its Three Oxidation States at Cryogenictemperatures Authors: Watt, W. / Tulinsky, A. / Swenson, R.P. / Watenpaugh, K.D. #2: ![]() Title: Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough) Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P. #3: ![]() Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough Authors: Curley, G.P. / Voordouw, G. #4: ![]() Title: The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0- Angstroms Resolution Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. #5: ![]() Title: Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.4 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 548.9 KB | Display | ![]() |
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Full document | ![]() | 564.7 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fx2S 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.38919, -0.92107, 0.01285), Vector: |
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Components
#1: Protein | Mass: 15704.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 ...Details: CRYSTALS WERE GROWN USING THE HANGING DROP METHOD OF VAPOUR DIFFUSION FROM TRIALS WITH AMMONIUM SULPHATE IN THE CONCENTRATION RANGE 60-80% SATURATION IN 50MM SODIUM PHOSPHATE BUFFER PH 8.0 CONTAINING 1MM EDTA WITH A PROTEIN CONCENTRATION OF 10-15MG/ML. CRYSTALS APPEAR OVER 1-3 DAYS., pH 7.0 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 55 % | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→20 Å / Num. obs: 26539 / % possible obs: 79.9 % / Observed criterion σ(I): -3 / Redundancy: 1.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5 / % possible all: 83.2 |
Reflection | *PLUS Num. measured all: 72050 |
Reflection shell | *PLUS % possible obs: 83.2 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: WILD TYPE FLAVODOXIN COORDINATES NOT DEPOSITED [M.A.WALSH PH.D THESIS NATIONAL UNIVERSITY OF IRELAND (1994)] BUT ESSENTIALLY IDENTICAL TO PDB ENTRY 2FX2 Resolution: 1.83→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 0.08 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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