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Yorodumi- PDB-3u2h: Crystal structure of the C-terminal DUF1608 domain of the Methano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u2h | ||||||
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Title | Crystal structure of the C-terminal DUF1608 domain of the Methanosarcina acetivorans S-layer (MA0829) protein | ||||||
Components | S-layer protein MA0829 | ||||||
Keywords | STRUCTURAL PROTEIN / DUF1608 domain / cell envelop / surface layer / S-layer / UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information S-layer / cell wall organization / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Methanosarcina acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Chan, S. / Phan, T. / Ahn, C.J. / Shin, A. / Rohlin, L. / Gunsalus, R.P. / Arbing, M.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans. Authors: Arbing, M.A. / Chan, S. / Shin, A. / Phan, T. / Ahn, C.J. / Rohlin, L. / Gunsalus, R.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u2h.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u2h.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 3u2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u2h_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 3u2h_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 3u2h_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3u2h_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/3u2h ftp://data.pdbj.org/pub/pdb/validation_reports/u2/3u2h | HTTPS FTP |
-Related structure data
Related structure data | 3u2gSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the full-length natural protein consists of a tandem repeats of two DUF1608 domains of highly similar sequences |
-Components
#1: Protein | Mass: 32108.582 Da / Num. of mol.: 1 / Fragment: C-terminal DUF1608 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0829, MA_0829 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q8TSG7 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2M sodium sulfate, 20% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal monochromator (Kohzu HLD8-24 Monochromator) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→90 Å / Num. obs: 12345 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rsym value: 0.096 / Χ2: 1.01 / Net I/σ(I): 12.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3U2G Resolution: 2.36→81.6 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 14.332 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 48.71 Å2 / Biso mean: 30.983 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→81.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.361→2.422 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 10.0717 Å / Origin y: -22.4895 Å / Origin z: 15.607 Å
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Refinement TLS group |
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