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Yorodumi- PDB-3bpd: Crystal structure of an uncharacterized protein (O28723_ARCFU) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bpd | ||||||
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Title | Crystal structure of an uncharacterized protein (O28723_ARCFU) from Archaeoglobus fulgidus | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / heptamer / Mg+2 ion / 10197b / PSI-2 / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | MTH889-like domain / Protein of unknown function DUF211 / MTH889-like domain superfamily / Uncharacterized ArCR, COG1888 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Eswaramoorthy, S. / Burley, S.K. / Sauder, J.M. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized protein (O28723_ARCFU) from Archaeoglobus fulgidus. Authors: Eswaramoorthy, S. / Burley, S.K. / Sauder, J.M. / Swaminathan, S. | ||||||
History |
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Remark 600 | HETEROGEN WATER MOLECULE HOH L125 IS IN CONTACT (3.18 A) WITH A MAGNESIUM ION MG L108 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bpd.cif.gz | 252.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bpd.ent.gz | 206 KB | Display | PDB format |
PDBx/mmJSON format | 3bpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bpd_validation.pdf.gz | 533.6 KB | Display | wwPDB validaton report |
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Full document | 3bpd_full_validation.pdf.gz | 561.3 KB | Display | |
Data in XML | 3bpd_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 3bpd_validation.cif.gz | 64.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bpd ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bpd | HTTPS FTP |
-Related structure data
Related structure data | 2raqS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11236.570 Da / Num. of mol.: 14 / Fragment: Residues 2-90 / Mutation: L70M 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_1549 / Production host: Escherichia coli (E. coli) / References: UniProt: O28723 #2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.82 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% PEG MME 550, 0.05M Magnesium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2007 / Details: Mirrors |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 60536 / Num. obs: 60536 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.9 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RAQ Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The Friedel pairs were used in phasing. 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 ...Details: The Friedel pairs were used in phasing. 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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Displacement parameters | Biso mean: 36.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026
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