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- PDB-5vrv: 2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vrv | ||||||
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Title | 2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative Lysylphosphatidylglycerol Synthetase from Agrobacterium fabrum. | ||||||
![]() | Protein regulated by acid pH | ||||||
![]() | HYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DUF2156 | ||||||
Function / homology | ![]() lysyltransferase / phosphatidylglycerol lysyltransferase activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative Lysylphosphatidylglycerol Synthetase from Agrobacterium fabrum. Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 744.3 KB | Display | ![]() |
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PDB format | ![]() | 643.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.2 KB | Display | ![]() |
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Full document | ![]() | 491.2 KB | Display | |
Data in XML | ![]() | 69.5 KB | Display | |
Data in CIF | ![]() | 98.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37139.137 Da / Num. of mol.: 6 / Fragment: residues 540-866 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: lpiA, Atu2521 / Plasmid: pMCSG53 / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 70.0 mg/ml, 0.01M HEPES (pH 7.5), Screen: 0.2M Potassium citrate, 0.3M 3-(1-Pyridinio)-1-propanesulfonate, 20% (w/v) P3350 20% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 133171 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.039 / Rsym value: 0.084 / Χ2: 1.138 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6765 / CC1/2: 0.694 / Rpim(I) all: 0.38 / Rsym value: 0.775 / Χ2: 1.002 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.957 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→29.65 Å
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Refine LS restraints |
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