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Yorodumi- PDB-1mjo: METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mjo | ||||||
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Title | METHIONINE HOLOREPRESSOR MUTANT (Q44K) PLUS COREPRESSOR (S-ADENOSYL METHIONINE) COMPLEXED TO THE MINIMAL MET CONSENSUS OPERATOR WITH THE CENTRAL TA STEP MUTATED TO AT | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / METJ / METHIONINE REPRESSOR / SHEET-HELIX-HELIX / S-ADENOSYL METHIONINE / DNA / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information methionine biosynthetic process / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Garvie, C.W. / Phillips, S.E.V. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Direct and indirect readout in mutant Met repressor-operator complexes. Authors: Garvie, C.W. / Phillips, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mjo.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mjo.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 1mjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mjo_validation.pdf.gz | 566.7 KB | Display | wwPDB validaton report |
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Full document | 1mjo_full_validation.pdf.gz | 591.2 KB | Display | |
Data in XML | 1mjo_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1mjo_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mjo ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mjo | HTTPS FTP |
-Related structure data
Related structure data | 1mj2C 1mjmC 1mjpC 1mjqC 1cmaS 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: DNA chain | Mass: 5819.784 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 12028.607 Da / Num. of mol.: 4 / Mutation: Q44K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: METJ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8U6 #3: Chemical | ChemComp-SAM / #4: Chemical | ChemComp-CA / | #5: 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: 2.92 Å3/Da / Density % sol: 58 % Description: THE FULL METJ COMPLEX WAS USED AS A SEARCH MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN (10MG/ML) + SAM (1MG/ML) + DNA (4MG/ML) WAS CRYSTALLISED FROM 28-38% MPD, 100MM SODIUM CACODYLATE BUFFER, PH 6.0-7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.5 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: PLATINUM COATED MIRROR |
Radiation | Monochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→31.8 Å / Num. obs: 199709 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.201 / % possible all: 100 |
Reflection | *PLUS Num. obs: 42229 / Num. measured all: 199709 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.201 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CMA Resolution: 2.1→31.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→31.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.86 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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