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Yorodumi- PDB-8egk: Re-refinement of Crystal Structure of NosGet3d, the All4481 prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8egk | |||||||||||||||||||||
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Title | Re-refinement of Crystal Structure of NosGet3d, the All4481 protein from Nostoc sp. PCC 7120 | |||||||||||||||||||||
Components | All4481 protein | |||||||||||||||||||||
Keywords | CHAPERONE / P-loop ATPase / Get3 / alpha-crystallin / cyanobacteria | |||||||||||||||||||||
Function / homology | : / ArsA, HSP20-like domain / HSP20-like domain found in ArsA / Anion-transporting ATPase-like domain / Anion-transporting ATPase / HSP20-like chaperone / P-loop containing nucleoside triphosphate hydrolase / AZIDE ION / All4481 protein Function and homology information | |||||||||||||||||||||
Biological species | Nostoc sp. PCC 7120 = FACHB-418 (bacteria) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å | |||||||||||||||||||||
Authors | Barlow, A.N. / Manu, M.S. / Ramasamy, S. / Clemons Jr., W.M. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis. Authors: Barlow, A.N. / Manu, M.S. / Saladi, S.M. / Tarr, P.T. / Yadav, Y. / Thinn, A.M.M. / Zhu, Y. / Laganowsky, A.D. / Clemons Jr., W.M. / Ramasamy, S. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / ...Authors: Liebschner, D. / Afonine, P.V. / Baker, M.L. / Bunkoczi, G. / Chen, V.B. / Croll, T.I. / Hintze, B. / Hung, L.W. / Jain, S. / McCoy, A.J. / Moriarty, N.W. / Oeffner, R.D. / Poon, B.K. / Prisant, M.G. / Read, R.J. / Richardson, J.S. / Richardson, D.C. / Sammito, M.D. / Sobolev, O.V. / Stockwell, D.H. / Terwilliger, T.C. / Urzhumtsev, A.G. / Videau, L.L. / Williams, C.J. / Adams, P.D. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8egk.cif.gz | 338.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8egk.ent.gz | 226.2 KB | Display | PDB format |
PDBx/mmJSON format | 8egk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8egk_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 8egk_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 8egk_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 8egk_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/8egk ftp://data.pdbj.org/pub/pdb/validation_reports/eg/8egk | HTTPS FTP |
-Related structure data
Related structure data | 8elfC 3igfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41582.953 Da / Num. of mol.: 2 / Mutation: A127T Source method: isolated from a genetically manipulated source Details: C-terminal His6 purification tag Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all4481 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YNT0 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 100mM MES (pH 6.15), 18% PEG3350, and 100mM potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2009 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→27.52 Å / Num. obs: 110202 / % possible obs: 89.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.11 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.288 / Num. unique obs: 11087 / Rsym value: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3IGF Resolution: 1.98→27.52 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.2305 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→27.52 Å
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Refine LS restraints |
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LS refinement shell |
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