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Yorodumi- PDB-1gto: HIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLE PROTEIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gto | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLE PROTEIN MUTANT | ||||||
Components | ROP | ||||||
Keywords | TRANSCRIPTION REGULATION / TURN / HELIX PACKING / CRYSTAL CONTACTS | ||||||
Function / homology | Helix Hairpins - #230 / Regulatory protein Rop / Rop-like superfamily / Rop protein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å | ||||||
Authors | Agrawal, V. / Predki, P. / Regan, L. / Brunger, A.T. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Amino-acid substitutions in a surface turn modulate protein stability. Authors: Predki, P.F. / Agrawal, V. / Brunger, A.T. / Regan, L. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Amino-Acid Substitutions in a Surface Turn Modulate Protein Stability Authors: Predki, P.F. / Agrawal, V. / Brunger, A.T. / Regan, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gto.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gto.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gto_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 1gto_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 1gto_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 1gto_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/1gto ftp://data.pdbj.org/pub/pdb/validation_reports/gt/1gto | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | THREE ROP PROTOMERS ARE IN THE ASYMMETRIC UNIT, TWO OF WHICH ARE RELATED BY A NON-CRYSTALLOGRAPHIC TWO-FOLD RELATIONSHIP FORMING A ROP DIMER (B/C). THE THIRD ROP PROTOMER (A) FORMS ANOTHER ROP DIMER THROUGH A CRYSTALLOGRAPHIC SYMMETRY MATE. |
-Components
#1: Protein | Mass: 6991.702 Da / Num. of mol.: 3 / Mutation: M1G, D30G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03051 #2: Water | ChemComp-HOH / | Compound details | THE HYPERSTABLE MUTANT, ROP D30G, SHOWED LITTLE INTRAMOLECULAR CHANGE FROM WILD TYPE. THE R.M.S ...THE HYPERSTABL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: unknown / Details: Banner, D.W., (1987) J. Mol. Biol., 196, 657. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Redundancy: 9 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.049 |
Reflection | *PLUS Highest resolution: 1.82 Å / Lowest resolution: 20 Å / Num. obs: 17635 / % possible obs: 98.9 % |
Reflection shell | *PLUS Highest resolution: 1.82 Å / Lowest resolution: 1.87 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.241 |
-Processing
Software |
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Refinement | Resolution: 1.82→20 Å / Rfactor Rfree error: 0.008 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.82→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.9 Å / Rfactor Rfree error: 0.024
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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