+Open data
-Basic information
Entry | Database: PDB / ID: 3but | ||||||
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Title | Crystal structure of protein Af_0446 from Archaeoglobus fulgidus | ||||||
Components | Uncharacterized protein Af_0446 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / LIPID BINDING PROTEIN / BETA BARREL / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å | ||||||
Authors | Bonanno, J.B. / Patskovsky, Y. / Ozyurt, S. / Ashok, S. / Zhang, F. / Groshong, C. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of protein Af_0446 from Archaeoglobus fulgidus. Authors: Bonanno, J.B. / Patskovsky, Y. / Ozyurt, S. / Ashok, S. / Zhang, F. / Groshong, C. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3but.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3but.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 3but.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3but_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
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Full document | 3but_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | 3but_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 3but_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3but ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3but | 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 | AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION. |
-Components
#1: Protein | Mass: 15424.122 Da / Num. of mol.: 1 / Mutation: K62A, K64A, L78I, I104V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: AF_0446 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: O29803 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 35mM Proline, 200mM Sodium formate, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2007 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 9264 / % possible obs: 99.6 % / Observed criterion σ(I): -0.5 / Redundancy: 7.5 % / Biso Wilson estimate: 34.66 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 0.8 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.91→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.517 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPY CORRECTION WAS APPLIED TO DIFFRACTION DATA. 3. UNDEFINED LIGAND OR COFACTOR IS BOUND INTO THE CENTRAL CAVITY, A PART OF IT ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPY CORRECTION WAS APPLIED TO DIFFRACTION DATA. 3. UNDEFINED LIGAND OR COFACTOR IS BOUND INTO THE CENTRAL CAVITY, A PART OF IT IS MOST LIKELY A LIPID. THIS LIGAND HAS NOT BEEN MODELED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.5 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.881 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.96 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -17.638 Å / Origin y: 7.91 Å / Origin z: -8.006 Å
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