+Open data
-Basic information
Entry | Database: PDB / ID: 3o3k | ||||||
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Title | Crystal structure of AF1382 from Archaeoglobus fulgidus | ||||||
Components | Uncharacterized protein AF_1382 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Southeast Collaboratory for Structural Genomics / sulfur phasing / SECSG / Protein Structure Initiative | ||||||
Function / homology | Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein AF_1382 Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Sulfur SAD / Resolution: 2.3 Å | ||||||
Authors | Zhu, J.-Y. / Zhao, M. / Fu, Z.-Q. / Yang, H. / Chang, J. / Xu, H. / Chen, L. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal. Authors: Zhu, J.Y. / Fu, Z.Q. / Chen, L. / Xu, H. / Chrzas, J. / Rose, J. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o3k.cif.gz | 30.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o3k.ent.gz | 20 KB | Display | PDB format |
PDBx/mmJSON format | 3o3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o3k ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o3k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11159.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1382 / Plasmid: pDEST-527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RPX / References: UniProt: O28889 |
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#2: 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: THE LAST REPRESENTS MERGED DATA SET |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.5 Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (2.8 MG/ML) AND SOLUTION CONTAING 0.1M SODIUM CITRATE/CITRIC ACID PH 5.5, 0.1M SODIUM CHLORIDE, 0.1M LITHIUM ...Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (2.8 MG/ML) AND SOLUTION CONTAING 0.1M SODIUM CITRATE/CITRIC ACID PH 5.5, 0.1M SODIUM CHLORIDE, 0.1M LITHIUM SULPHATE, 30% V/V PEG 400, Microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 2007 / Details: ROSENBAUM |
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 5325 / % possible obs: 99.9 % / Redundancy: 25 % / Biso Wilson estimate: 37.5 Å2 / Rsym value: 0.045 / Net I/σ(I): 124.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 17.4 / Num. unique all: 5325 / Rsym value: 0.254 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: Sulfur SAD / Resolution: 2.3→37.86 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 160315.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.7117 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→37.86 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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