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Yorodumi- PDB-1mjk: METHIONINE REPRESSOR MUTANT APOREPRESSOR (Q44K) FROM ESCHERICHIA COLI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mjk | ||||||
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Title | METHIONINE REPRESSOR MUTANT APOREPRESSOR (Q44K) FROM ESCHERICHIA COLI | ||||||
Components | METHIONINE REPRESSOR | ||||||
Keywords | TRANSCRIPTION REGULATION / METJ / REPRESSOR / SHEET-HELIX-HELIX | ||||||
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 / DIFFERENCE FOURIER METHODS / Resolution: 2.15 Å | ||||||
Authors | Garvie, C.W. / Phillips, S.E.V. | ||||||
Citation | Journal: Thesis, University of Leeds / Year: 1997 Title: Crystallographic studies of the methionine repressor-operator complex and the oc31 42kDa repressor Authors: Garvie, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mjk.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mjk.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/1mjk ftp://data.pdbj.org/pub/pdb/validation_reports/mj/1mjk | HTTPS FTP |
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-Related structure data
Related structure data | 1cmbS 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: 12028.607 Da / Num. of mol.: 2 / 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 #2: Chemical | ChemComp-PO4 / | #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: 2.06 Å3/Da / Density % sol: 40 % |
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 16-28% PEG 600, 1.5% NAIO4, 100MM POTASSIUM PHOSPHATE BUFFER, PH 7.0. |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→23 Å / Num. obs: 10414 / % possible obs: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.205 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER METHODS Starting model: PDB ENTRY 1CMB Resolution: 2.15→23 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 30.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.223 / Rfactor Rwork: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.293 / Rfactor Rwork: 0.23 |