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- PDB-2p5d: Crystal structure of MJECL36 from Methanocaldococcus jannaschii D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p5d | ||||||
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Title | Crystal structure of MJECL36 from Methanocaldococcus jannaschii DSM 2661 | ||||||
![]() | UPF0310 protein MJECL36 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Methanocaldococcus jannaschii / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Uncharacterised protein family UPF0310 / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta / UPF0310 protein MJECL36![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of MJECL36 from Methanocaldococcus jannaschii DSM 2661 Authors: Sugahara, M. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.6 KB | Display | ![]() |
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PDB format | ![]() | 32.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424 KB | Display | ![]() |
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Full document | ![]() | 426 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wmmS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is monomer in the asymmetric. |
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Components
#1: Protein | Mass: 17574.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET-21a / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.88 % |
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Crystal grow | Temperature: 291 K / Method: oil microbatch / pH: 5.5 Details: 27.5% PEG 4000, 0.1M Acetate-NaOH, 10% Dioxane, pH 5.5, oil microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 25, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 16540 / Num. obs: 16540 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.037 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1625 / Rsym value: 0.176 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WMM Resolution: 1.7→19.25 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→19.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.03
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