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Yorodumi- PDB-2p6c: Crystal structure of hypothetical protein aq_2013 from Aquifex ae... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p6c | ||||||
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Title | Crystal structure of hypothetical protein aq_2013 from Aquifex aeolicus VF5. | ||||||
Components | aq_2013 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | YjbQ-like / Uncharacterised protein family UPF0047, YjbQ / YjbQ-like superfamily / Uncharacterised protein family UPF0047 / Jelly Rolls / Sandwich / Mainly Beta / PHOSPHATE ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yamamoto, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of hypothetical protein aq_2013 from Aquifex aeolicus VF5 Authors: Yamamoto, 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 | 2p6c.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p6c.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p6c_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 2p6c_full_validation.pdf.gz | 452.2 KB | Display | |
Data in XML | 2p6c_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2p6c_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/2p6c ftp://data.pdbj.org/pub/pdb/validation_reports/p6/2p6c | HTTPS FTP |
-Related structure data
Related structure data | 1vmjS 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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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a trimer. |
-Components
#1: Protein | Mass: 16012.288 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O67812 #2: Chemical | ChemComp-PO4 / #3: 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: 1.99 Å3/Da / Density % sol: 38.05 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.6 Details: 0.1M Sodium Citrate, 1.0M Ammonium dihydrogen Phosphate, pH 5.6, MICROBATCH, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 16682 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 16.729 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.045 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 15 / Num. unique all: 1660 / Rsym value: 0.093 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VMJ Resolution: 2→35.12 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THOUGEOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.02
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