+Open data
-Basic information
Entry | Database: PDB / ID: 2q07 | ||||||
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Title | Crystal structure of AF0587, a protein of unknown function | ||||||
Components | Uncharacterized protein AF0587 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10391c / protein AF0587 / monomer / PSI-2 / Protein Structure Initiative / 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: 2.04 Å | ||||||
Authors | Sugadev, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of AF0587, a protein of unknown function. Authors: Sugadev, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q07.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q07.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 2q07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/2q07 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/2q07 | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 35277.723 Da / Num. of mol.: 1 / Fragment: Residues 233-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Species: Archaeoglobus fulgidus / Strain: VC-16, DSM 4304, JCM 9628, NBRC 100126 / Gene: AF_0587 / Plasmid: pSGX3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29668 |
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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: 1.94 Å3/Da / Density % sol: 36.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Magnesium formate, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 8, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 16046 / Num. obs: 16046 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.04→2.13 Å / Redundancy: 1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1 / % possible all: 52 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→32.04 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 95114.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.3266 Å2 / ksol: 0.379082 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→32.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.13 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
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Xplor file |
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