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- PDB-3bqt: Crystal structure of a protein of unknown function from Listeria ... -
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Open data
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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 | ||||||
![]() | Uncharacterized protein | ||||||
![]() | 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 / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Madegowda, M. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.9 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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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.) ![]() Species: Listeria monocytogenes / Strain: F2365 / Serotype 4b / Gene: LMOf2365_2733 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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