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- PDB-1rty: Crystal Structure of Bacillus subtilis YvqK, a putative ATP-bindi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rty | ||||||
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Title | Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin Adenosyltransferase, The North East Structural Genomics Target SR128 | ||||||
![]() | yvqk protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / all alpha-helical trimeric protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | ![]() corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Lee, I. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Functional insights from structural genomics. Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1sqsC ![]() 1tm0C ![]() 1zbpC ![]() 2hd3C ![]() 2nv4C ![]() 2oysC ![]() 1nogS 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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Unit cell |
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Details | the protein most likely functions as a trimer. |
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Components
#1: Protein | Mass: 21613.064 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.66 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 50 mM MES, 12% PEG 20,000 , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2003 | ||||||||||||
Radiation | Monochromator: monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→24.6 Å / Num. all: 46124 / Num. obs: 39984 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.108 / Net I/σ(I): 15 | ||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.99 / Num. unique all: 39984 / Rsym value: 0.283 / % possible all: 86.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NOG Resolution: 2.4→24.6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 304817.15 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber Details: Only the five N-terminal residues of the monomer B have clear density, as they have been modeled. However, prior to the initiating methionine of the monomer B, there is an additional density ...Details: Only the five N-terminal residues of the monomer B have clear density, as they have been modeled. However, prior to the initiating methionine of the monomer B, there is an additional density of an unrecognizable shape with the molecular mass of 100-150 Dalton. Our mass spectrum also reveals a peak, corresponding to 130 Dalton. Moreover, the unknown chemical entity possibly is covalently bound to the methionine.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.47 Å2 / ksol: 0.320189 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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