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Yorodumi- PDB-2eky: Crystal Structure of hypothetical protein MJ1052 from Methanocald... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eky | ||||||
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Title | Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii 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 | 2eky.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eky.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 2eky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eky_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 2eky_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 2eky_validation.xml.gz | 37 KB | Display | |
Data in CIF | 2eky_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/2eky ftp://data.pdbj.org/pub/pdb/validation_reports/ek/2eky | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11243.202 Da / Num. of mol.: 8 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: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.96 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: 50%(v/v) PEG200, 0.1M Tris, pH 7.0, microbatch, temperature 295K |
-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 | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. all: 68040 / Num. obs: 68040 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.065 / Net I/σ(I): 9.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6325 / Rsym value: 0.439 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LXN Resolution: 1.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1648422.06 / 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: 58.0032 Å2 / ksol: 0.357144 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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