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Yorodumi- PDB-1zkd: X-Ray structure of the putative protein Q6N1P6 from Rhodopseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zkd | ||||||
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Title | X-Ray structure of the putative protein Q6N1P6 from Rhodopseudomonas palustris at the resolution 2.1 A , Northeast Structural Genomics Consortium target RpR58 | ||||||
Components | DUF185 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / RpR58 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Kuzin, A.P. / Yong, W. / Vorobiev, S.M. / Acton, T. / Ma, L. / Xiao, R. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-Ray structure of the putative protein Q6N1P6 from Rhodopseudomonas palustris at the resolution 2.1 A , Northeast Structural Genomics Consortium target RpR58 Authors: Kuzin, A.P. / Yong, W. / Vorobiev, S.M. / Acton, T. / Ma, L. / Xiao, R. / Montelione, G. / 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 | 1zkd.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zkd.ent.gz | 122.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zkd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zkd ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zkd | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42821.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA4359 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q6N1P6 #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 | Density Matthews: 2.68 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 8.5 Details: 4m Ammonium Acetate, 0.1M Tris-HCl, pH 8.5, microbatch, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913, 0.97942, 0.96774 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2005 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→30 Å / Num. obs: 99268 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 15.3 Å2 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→22.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 230090.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.3738 Å2 / ksol: 0.34957 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→22.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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