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Yorodumi- PDB-2epi: Crystal Structure pf hypothetical protein MJ1052 from Methanocald... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2epi | ||||||
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Title | Crystal Structure pf hypothetical protein MJ1052 from Methanocaldococcus jannascii (Form 2) | ||||||
Components | UPF0045 protein MJ1052 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | : / Thiamine-binding protein / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / UPF0045 protein MJ1052 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure pf hypothetical protein MJ1052 from Methanocaldococcus jannascii Authors: Mizutani, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2epi.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2epi.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 2epi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2epi_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 2epi_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 2epi_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 2epi_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/2epi ftp://data.pdbj.org/pub/pdb/validation_reports/ep/2epi | HTTPS FTP |
-Related structure data
Related structure data | 1lxnS S: Starting model for refinement |
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Similar structure data | |
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: 11243.202 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSM 2661 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q58452 #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: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 30%(v/v) Jeffamine M-600, 0.1M HEPES, pH 7.0, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 9, 2007 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 41290 / Num. obs: 41290 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.042 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.24 / Num. unique all: 4121 / Rsym value: 0.302 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LXN Resolution: 1.7→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1036084.32 / 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: 47.9238 Å2 / ksol: 0.32183 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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