+Open data
-Basic information
Entry | Database: PDB / ID: 2iel | ||||||
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Title | CRYSTAL STRUCTURE OF TT0030 from Thermus Thermophilus | ||||||
Components | Hypothetical Protein TT0030 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / TT0030 / Thermus Thermophilus / PSI / PROTEIN STRUCTURE INITIATIVE / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG | ||||||
Function / homology | HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Zhu, J. / Huang, J. / Stepanyuk, G. / Chen, L. / Chang, J. / Zhao, M. / Xu, H. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF TT0030 from Thermus Thermophilus AT 1.6 ANGSTROMS RESOLUTION Authors: Zhu, J. / Huang, J. / Stepanyuk, G. / Chen, L. / Chang, J. / Zhao, M. / Xu, H. / Liu, Z.J. / Rose, J.P. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iel.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iel.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 2iel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iel_validation.pdf.gz | 431.3 KB | Display | wwPDB validaton report |
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Full document | 2iel_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 2iel_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 2iel_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/2iel ftp://data.pdbj.org/pub/pdb/validation_reports/ie/2iel | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 3 - 135 / Label seq-ID: 3 - 135
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Details | PISA SAYS THAT IS IS A A4B4 OCTOMER REPRESENTED BY A TWO LAYER TETRAMER |
-Components
#1: Protein | Mass: 15069.342 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT0030 / Plasmid: PET16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q72LM7 #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: 2.15 Å3/Da / Density % sol: 42.94 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 6.9 Details: MODIFIED MICROBATCH USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (28.3 mg/ml) AND SOLUTION CONTAING 10% GLYCEROL, 1.26M TR-ISODIUM CITRATE DIHYDRATE, 0.09M ...Details: MODIFIED MICROBATCH USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (28.3 mg/ml) AND SOLUTION CONTAING 10% GLYCEROL, 1.26M TR-ISODIUM CITRATE DIHYDRATE, 0.09M HEPES pH 7.5, Temperature 291K., pH 6.9, MICROBATCH UNDER OIL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2006 / Details: ROSENBAUM |
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 30385 / % possible obs: 71.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rsym value: 0.045 / Net I/σ(I): 57.1 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.77 / Num. unique all: 1291 / Rsym value: 0.28 / % possible all: 30.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→18.59 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.969 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.844 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→18.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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