+Open data
-Basic information
Entry | Database: PDB / ID: 1o7l | ||||||
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Title | Molybdate-activated form of ModE from Escherichia coli | ||||||
Components | TRANSCRIPTIONAL REGULATOR MODE | ||||||
Keywords | TRANSCRIPTION REGULATION / DNA BINDING / MOLYBDATE / MOP / WINGED HELIX-TURN-HELIX / TRANSCRIPTIONAL REGULATOR / ACTIVATOR | ||||||
Function / homology | Function and homology information ModE complex / molybdate ion transport / negative regulation of DNA-templated transcription initiation / molybdenum ion binding / cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Schuttelkopf, A.W. / Hunter, W.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal Structure of Activated Mode Reveals Conformational Changes Involving Both Oxyanion and DNA-Binding Domains Authors: Schuttelkopf, A.W. / Boxer, D.H. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o7l.cif.gz | 203.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o7l.ent.gz | 162.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o7l_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 1o7l_full_validation.pdf.gz | 506.2 KB | Display | |
Data in XML | 1o7l_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 1o7l_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/1o7l ftp://data.pdbj.org/pub/pdb/validation_reports/o7/1o7l | HTTPS FTP |
-Related structure data
Related structure data | 1h9rS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | BIOMOLECULE 1:BIOMOLECULE 2: |
-Components
#1: Protein | Mass: 28308.146 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PLAA6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46930, UniProt: P0A9G8*PLUS #2: Chemical | ChemComp-MOO / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Compound details | MODE-MO COMPLEX ACTS AS A REPRESSOR OF THE MODABCD OPERON THAT IS INVOLVED IN THE TRANSPORT OF ...MODE-MO COMPLEX ACTS AS A REPRESSOR OF THE MODABCD OPERON THAT IS INVOLVED IN THE TRANSPORT OF MOLYBDATE. BINDING OF MOLYBDENUM | |
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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: 2.68 Å3/Da / Density % sol: 54 % Description: THE DATA IS PARTIALLY MEROHEDRALLY TWINNED WITH A TWIN FRACTION OF APPROXIMATELY 0.33 AND A TWIN LAW OF H, -K, -L. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 27% PEG1000, 70MM CACL2, 1.5% 1,2,3-HEPTANETRIOL, 70MM HEPES PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 15, 1999 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→25 Å / Num. obs: 29920 / % possible obs: 96 % / Redundancy: 4.6 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.75→2.81 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.8 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 2992 / Num. measured all: 124769 |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H9R Resolution: 2.75→25 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.1093 Å2 / ksol: 0.264797 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 1.38 Å / Weight position: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.85 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.255 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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