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Yorodumi- PDB-1yo7: Re-engineering topology of the homodimeric ROP protein into a sin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yo7 | ||||||
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Title | Re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle | ||||||
Components | Regulatory protein rop | ||||||
Keywords | REPLICATION REGULATOR / Protein design / re-engineering of topology / four-helix bundle | ||||||
Function / homology | Regulatory protein Rop / Rop-like superfamily / Rop protein / Alpha-catenin/vinculin-like / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / identical protein binding / Regulatory protein rop Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SIR, model building / Resolution: 2.8 Å | ||||||
Authors | Sagermann, M. / Emery, S.C. / Sander, C. | ||||||
Citation | Journal: To be Published Title: Re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle. Authors: Sagermann, M. / Emery, S.C. / Sander, C. #1: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of the ColE1 rop protein at 1.7 A resolution Authors: Banner, D.W. / Kokkinidis, M. / Tsernoglou, D. | ||||||
History |
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Remark 999 | SEQUENCE Residues 1-56 were taken from wild type ROP (except for R55S), a new Loop-B (residues ...SEQUENCE Residues 1-56 were taken from wild type ROP (except for R55S), a new Loop-B (residues KKNGQI) was added, then residues 32-56 were added subsequently followed by the new Loop-C (sequence GGS). Finally, wild type ROP residues 3-29 and a terminal AKG sequence were added. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yo7.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yo7.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yo7_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 1yo7_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 1yo7_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1yo7_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yo7 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yo7 | HTTPS FTP |
-Related structure data
Related structure data | 1ropS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13695.465 Da / Num. of mol.: 2 / Mutation: R55S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: The gene for LMROP2 was artificially assembled using cassette mutagenesis and c loned into the expression vector Gene: rop / Plasmid: pEX70 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: P03051 #2: Chemical | ChemComp-ZN / | #3: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 10% PEG 2000, 50mM Tris-HCl pH6.6, 40mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 4, 1994 |
Radiation | Monochromator: Graphite, NI Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→26.4 Å / Num. all: 5376 / Num. obs: 5376 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.74 Å2 |
Reflection shell | Resolution: 2.8→2.98 Å / Num. unique all: 783 / Rsym value: 0.11 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: SIR, model building Starting model: PDb entry 1ROP Resolution: 2.8→26.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Data were collected from very flat, plate-like crystals. Only partially occupied platinum atoms could be used to calculate preliminary phases. These initial HA positions were used in ...Details: Data were collected from very flat, plate-like crystals. Only partially occupied platinum atoms could be used to calculate preliminary phases. These initial HA positions were used in combination with molecular replacement to determine the structure.
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→26.4 Å
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Refine LS restraints |
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