+Open data
-Basic information
Entry | Database: PDB / ID: 1p8c | ||||||
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Title | Crystal structure of TM1620 (APC4843) from Thermotoga maritima | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / 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 / SAD / Resolution: 2.3 Å | ||||||
Authors | Kim, Y. / Joachimiak, A. / Brunzelle, J.S. / Korolev, S.V. / Edwards, A. / Xu, X. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure Analysis of Thermotoga maritima protein TM1620 (APC4843) Authors: Kim, Y. / Joachimiak, A. / Brunzelle, J.S. / Korolev, S.V. / Edwards, A. / Xu, X. / Savchenko, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS. THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p8c.cif.gz | 144.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8c.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 1p8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p8c_validation.pdf.gz | 484.1 KB | Display | wwPDB validaton report |
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Full document | 1p8c_full_validation.pdf.gz | 515.4 KB | Display | |
Data in XML | 1p8c_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 1p8c_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8c ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8c | 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: 16523.871 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1V5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: potassium citrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.15→50 Å / Num. all: 39155 / Num. obs: 39155 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3655 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→48.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 153151.96 / Data cutoff high rms absF: 153151.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.7314 Å2 / ksol: 0.329463 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→48.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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