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Yorodumi- PDB-3bqt: Crystal structure of a protein of unknown function from Listeria ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bqt | ||||||
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Title | Crystal structure of a protein of unknown function from Listeria monocytogenes, tetragonal form | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10114f / NYSGXRC / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / : Function and homology information | ||||||
Biological species | Listeria monocytogenes str. 4b F2365 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Madegowda, M. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a protein of unknown function from Listeria monocytogenes. Authors: Madegowda, M. / Sauder, J.M. / 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 | 3bqt.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bqt.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/3bqt ftp://data.pdbj.org/pub/pdb/validation_reports/bq/3bqt | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 10630.845 Da / Num. of mol.: 2 / Mutation: G27V, L50M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes str. 4b F2365 (bacteria) Species: Listeria monocytogenes / Strain: F2365 / Serotype 4b / Gene: LMOf2365_2733 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q71W18 #2: 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: 2.54 Å3/Da / Density % sol: 51.67 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M MgCl2, 0.1M Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 2, 2007 / Details: SGX-CAT |
Radiation | Monochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30.77 Å / Num. all: 9166 / Num. obs: 9166 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 26.2 % / Biso Wilson estimate: -0.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 27.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 14.4 / Num. unique all: 1458 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→26.04 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 121956.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 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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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.337389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→26.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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