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Yorodumi- PDB-3mnf: Crystal structure of PAC2 family protein from Streptomyces avermi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mnf | ||||||
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Title | Crystal structure of PAC2 family protein from Streptomyces avermitilis MA | ||||||
Components | PAC2 family protein | ||||||
Keywords | structural genomics / unknown function / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Rv2714-like / PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å | ||||||
Authors | Chang, C. / Hatzos, C. / Morgan, T. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PAC2 family protein from Streptomyces avermitilis MA Authors: Chang, C. / Hatzos, C. / Morgan, T. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mnf.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mnf.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mnf_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 3mnf_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 3mnf_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 3mnf_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/3mnf ftp://data.pdbj.org/pub/pdb/validation_reports/mn/3mnf | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | hexamer with operators (x,y,z), (-y+1,x-y,z), (-x+y+1,-x+1,z), (-y+1,-x+1,-z+1/2), (x,x-y,-z+1/2), (-x+y+1,y,-z+1/2) |
-Components
#1: Protein | Mass: 27381.268 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: SAV6650, SAV_6650 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q828L9 |
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#2: Chemical | ChemComp-CL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.23 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.0M Na/K tartrate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2010 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→50 Å / Num. all: 11041 / Num. obs: 10559 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 41.5 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 4.84 / Num. unique all: 507 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.919 / SU B: 26.757 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.5 / ESU R Free: 0.306 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 88.778 Å2
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Refinement step | Cycle: LAST / Resolution: 2.97→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.975→3.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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