+Open data
-Basic information
Entry | Database: PDB / ID: 1kr4 | ||||||
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Title | Structure Genomics, Protein TM1056, cutA | ||||||
Components | Protein TM1056, cutA | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / cutA / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å | ||||||
Authors | Savchenko, A. / Zhang, R. / Joachimiak, A. / Edwards, A. / Akarina, T. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: X-ray crystal structure of CutA from Thermotoga maritima at 1.4 A resolution. Authors: Savchenko, A. / Skarina, T. / Evdokimova, E. / Watson, J.D. / Laskowski, R. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A. / Zhang, R.G. | ||||||
History |
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Remark 999 | SEQUENCE The assignement of Ile94 was based on high resolution electron density maps |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kr4.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kr4.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kr4_validation.pdf.gz | 362.8 KB | Display | wwPDB validaton report |
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Full document | 1kr4_full_validation.pdf.gz | 366.4 KB | Display | |
Data in XML | 1kr4_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1kr4_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1kr4 ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1kr4 | HTTPS FTP |
-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: 15021.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) Plasmid details: Protein was expressed as fusion with N-terminal tag MGSSHHHHHHSSGRENLYFQGHM and C-terminal fusion of GS Plasmid: modified peT15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X0E6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.7 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 / Details: Zhang, R.G., (2001) Structure, 9, 1095. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,0.9791,0.95200 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 20, 2001 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→50 Å / Num. all: 20453 / Num. obs: 19451 / % possible obs: 95.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.49 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 24.25 | ||||||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.875 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.66 / Num. unique all: 1829 / % possible all: 87.7 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→20.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 485887.96 / Data cutoff high rms absF: 485887.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.9317 Å2 / ksol: 0.389531 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→20.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 40 Å / Num. reflection obs: 19651 / σ(F): 0 / Rfactor Rfree: 0.2408 / Rfactor Rwork: 0.2094 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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