+Open data
-Basic information
Entry | Database: PDB / ID: 1q4r | ||||||
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Title | Gene Product of At3g17210 from Arabidopsis Thaliana | ||||||
Components | protein At3g17210 | ||||||
Keywords | UNKNOWN FUNCTION / STRUCTURAL GENOMICS / Arabidopsis Thaliana / Center for Eukaryotic Structural Genomics / Protein Structure Initiative / CESG | ||||||
Function / homology | Function and homology information pollen tube adhesion / defense response to fungus / defense response to bacterium / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Phillips Jr., G.N. / Bingman, C.A. / Johnson, K.A. / Smith, D.W. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana Authors: Bingman, C.A. / Johnson, K.A. / Peterson, F.C. / Frederick, R.O. / Zhao, Q. / Thao, S. / Fox, B.G. / Volkman, B.F. / Jeon, W.B. / Smith, D.W. / Newman, C.S. / Ulrich, E.L. / Hegeman, A. / ...Authors: Bingman, C.A. / Johnson, K.A. / Peterson, F.C. / Frederick, R.O. / Zhao, Q. / Thao, S. / Fox, B.G. / Volkman, B.F. / Jeon, W.B. / Smith, D.W. / Newman, C.S. / Ulrich, E.L. / Hegeman, A. / Sussman, M.R. / Markley, J.L. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q4r.cif.gz | 32.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q4r.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 1q4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q4r_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 1q4r_full_validation.pdf.gz | 418.2 KB | Display | |
Data in XML | 1q4r_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 1q4r_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q4r ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q4r | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis:-x, -y, z and a translation of 0 1 0 |
-Components
#1: Protein | Mass: 12576.025 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g17210 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9LUV2 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Sodium MES, Sodium citrate, MEthyl Ether PEG 5000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003 / Details: Bent cylindrical Si-mirror (Rh coating) |
Radiation | Monochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 7570 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.06 / Num. unique all: 598 / % possible all: 75.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 14162 / % possible obs: 93.5 % / Redundancy: 5.2 % / Num. measured all: 75176 |
Reflection shell | *PLUS % possible obs: 52.6 % / Rmerge(I) obs: 0.274 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.331 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.214 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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