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Yorodumi- PDB-1lrh: Crystal structure of auxin-binding protein 1 in complex with 1-na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lrh | |||||||||
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Title | Crystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid | |||||||||
Components | auxin-binding protein 1 | |||||||||
Keywords | PROTEIN BINDING / BETA JELLYROLL / DOUBLE STRANDED PARALLEL BETA HELIX / GERMIN LIKE PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of DNA endoreduplication / cytokinesis by cell plate formation / auxin binding / unidimensional cell growth / auxin-activated signaling pathway / positive regulation of cell division / positive regulation of cell size / endoplasmic reticulum lumen / zinc ion binding Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / difference fourier / Resolution: 1.9 Å | |||||||||
Authors | Woo, E.J. / Marshall, J. / Bauly, J. / Chen, J.-G. / Venis, M. / Napier, R.M. / Pickersgill, R.W. | |||||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Crystal structure of auxin-binding protein 1 in complex with auxin. Authors: Woo, E.J. / Marshall, J. / Bauly, J. / Chen, J.G. / Venis, M. / Napier, R.M. / Pickersgill, R.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lrh.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lrh.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lrh_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1lrh_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1lrh_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 1lrh_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/1lrh ftp://data.pdbj.org/pub/pdb/validation_reports/lr/1lrh | HTTPS FTP |
-Related 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: 18411.809 Da / Num. of mol.: 4 / Mutation: D161E/E162Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: ABP1 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P13689 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-NLA / #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: 2.4 Å3/Da / Density % sol: 48.81 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 7 Details: Woo, E.J., (2000) Acta Crystallogr., Sect.D, 56, 1476. | |||||||||||||||||||||||||||||||||||
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: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 54476 / Num. obs: 53495 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.096 / % possible all: 90 |
Reflection | *PLUS % possible obs: 94.2 % |
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: difference fourier / Resolution: 1.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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