+Open data
-Basic information
Entry | Database: PDB / ID: 1ne2 | ||||||
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Title | Crystal Structure of Thermoplasma acidophilum 1320 (APC5513) | ||||||
Components | hypothetical protein ta1320 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / autoSHARP / Resolution: 1.75 Å | ||||||
Authors | Kim, Y. / Joachimiak, A. / Edwards, A. / Xu, X. / Christendat, D. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Thermoplasma acidophilum 1320 (APC5513) Authors: Kim, Y. / Joachimiak, A. / Edwards, A. / Xu, X. / Christendat, D. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN BUT APPEARS TO BE A DIMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ne2.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ne2.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ne2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ne2_validation.pdf.gz | 447.7 KB | Display | wwPDB validaton report |
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Full document | 1ne2_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 1ne2_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1ne2_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1ne2 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1ne2 | 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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Details | unknown but it appears a dimer. |
-Components
#1: Protein | Mass: 22681.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta1320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HIL9 #2: Chemical | ChemComp-FMT / | #3: 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: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium acetate, PEG 4000, Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: 1.75→40.47 Å / Num. all: 40030 / Num. obs: 40030 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 7.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3 / Num. unique all: 3918 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: autoSHARP / Resolution: 1.75→40.47 Å / Rfactor Rfree error: 0.004 / 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: 48.279 Å2 / ksol: 0.37745 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.23 Å / Luzzati sigma a free: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→40.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.83 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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