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Yorodumi- PDB-6lkb: Crystal Structure of the peptidylprolyl isomerase domain of Arabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lkb | ||||||
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Title | Crystal Structure of the peptidylprolyl isomerase domain of Arabidopsis thaliana CYP71. | ||||||
Components | Peptidyl-prolyl cis-trans isomerase CYP71 | ||||||
Keywords | ISOMERASE / PPIASE / CYP71 / cyclophilin / chromatin remodelling | ||||||
Function / homology | Function and homology information : / carpel development / sepal formation / meristem structural organization / leaf formation / regulation of root meristem growth / leaf shaping / stamen development / regulation of flower development / leaf vascular tissue pattern formation ...: / carpel development / sepal formation / meristem structural organization / leaf formation / regulation of root meristem growth / leaf shaping / stamen development / regulation of flower development / leaf vascular tissue pattern formation / protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / histone binding / chromatin binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å | ||||||
Authors | Lakhanpal, S. / Jobichen, C. / Swaminathan, K. | ||||||
Citation | Journal: Febs Lett. / Year: 2021 Title: Structural and functional analyses of the PPIase domain of Arabidopsis thaliana CYP71 reveal its catalytic activity toward histone H3. Authors: Lakhanpal, S. / Fan, J.S. / Luan, S. / Swaminathan, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lkb.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lkb.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 6lkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lkb_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
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Full document | 6lkb_full_validation.pdf.gz | 463.8 KB | Display | |
Data in XML | 6lkb_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6lkb_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lkb ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lkb | HTTPS FTP |
-Related structure data
Related structure data | 2a2nS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18149.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP71, At3g44600, F14L2.150 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8W4D0, peptidylprolyl isomerase |
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-Non-polymers , 5 types, 321 molecules
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3.25 Å3/Da / Density % sol: 62.15 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES (pH 6.5), 1.5M ammonium sulphate, 0.02M cobalt chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30.48 Å / Num. obs: 57328 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 19.41 Å2 / CC1/2: 0.85 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.65→1.69 Å / Num. unique obs: 3778 / CC1/2: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2a2n Resolution: 1.651→30.477 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.61 Å2 / Biso mean: 24.4805 Å2 / Biso min: 13.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.651→30.477 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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