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Yorodumi- PDB-1fya: CRYSTAL STRUCTURE OF THE HEXA-SUBSTITUTED MUTANT OF THE MOLECULAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fya | ||||||
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Title | CRYSTAL STRUCTURE OF THE HEXA-SUBSTITUTED MUTANT OF THE MOLECULAR CHAPERONIN GROEL APICAL DOMAIN | ||||||
Components | 60 KD CHAPERONIN | ||||||
Keywords | CHAPERONE / Stabilizing mutant | ||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Wang, Q. / Buckle, A.M. / Fersht, A.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Stabilization of GroEL minichaperones by core and surface mutations. Authors: Wang, Q. / Buckle, A.M. / Fersht, A.R. #1: Journal: Protein Sci. / Year: 1999 Title: Design of Highly Stable Functional GroEL Minichaperones Authors: Wang, Q. / Buckle, A.M. / Foster, N.W. / Johnson, C.M. / Fersht, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fya.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fya.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fya ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fya | HTTPS FTP |
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-Related structure data
Related structure data | 1fy9C 1kidS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20856.006 Da / Num. of mol.: 1 / Fragment: APICAL DOMAIN (RESIDUES 191-376) / Mutation: A212E/A223T/M233L/I305L/E308K/N326T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PRSET A / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 43 % | |||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.75-0.9 M SODIUM POTASSIUM TARTRATE, 50 MM MES SODIUM, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||
Crystal grow | *PLUS pH: 6.5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.963 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 8, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.963 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38.1 Å / Num. all: 10968 / Num. obs: 10757 / % possible obs: 93 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.22→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.4 / % possible all: 89.2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 38.1 Å / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Num. measured all: 41965 |
Reflection shell | *PLUS % possible obs: 89.2 % / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: GROEL(191-376) (PDB: 1KID) Resolution: 2.2→38.1 Å / SU B: 7.8 / SU ML: 0.19 / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.25 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.1 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 38.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |