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Yorodumi- PDB-3k9r: X-ray structure of the Rhodanese-like domain of the Alr3790 prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k9r | ||||||
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Title | X-ray structure of the Rhodanese-like domain of the Alr3790 protein from Anabaena sp. Northeast Structural Genomics Consortium Target NsR437c. | ||||||
Components | Alr3790 protein | ||||||
Keywords | structural genomics / unknown function / ALR3790 / RHODANESE-LIKE / NSR437C / NESG / STRUCTURAL GENOMICS. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Vorobiev, S. / Chen, Y. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Chen, Y. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray structure of the Rhodanese-like domain of the Alr3790 protein from Anabaena sp. Authors: Vorobiev, S. / Chen, Y. / Seetharaman, J. / Maglaqui, M. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k9r.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k9r.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3k9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k9r_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 3k9r_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 3k9r_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3k9r_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/3k9r ftp://data.pdbj.org/pub/pdb/validation_reports/k9/3k9r | HTTPS FTP |
-Related structure data
Related structure data | 3ilmS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | monomer according to aggregation screening; however likely dimer under crystallization conditions. |
-Components
#1: Protein | Mass: 12932.752 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) +MAGIC / References: UniProt: Q8YQN0 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: microbatch under parafin oil / pH: 4.5 Details: 25% PEG 3350, 0.1M sodium acetate, pH 4.5, MICROBATCH UNDER PARAFIN OIL, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2009 / Details: Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 52885 / Num. obs: 49871 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5315 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ILM Resolution: 1.96→36.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 382449.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.1714 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→36.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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