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Yorodumi- PDB-2wfj: Atomic resolution crystal structure of the PPIase domain of human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wfj | ||||||
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Title | Atomic resolution crystal structure of the PPIase domain of human cyclophilin G in complex with cyclosporin A. | ||||||
Components |
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Keywords | ISOMERASE/IMMUNOSUPPRESSANT / ISOMERASE-IMMUNOSUPPRESSANT COMPLEX / CYCLOPHILIN-CYCLOSPORIN COMPLEX / CYCLOSPORIN A / IMMUNOSUPPRESSANT / CYCLOPHILIN | ||||||
Function / homology | Function and homology information cyclosporin A binding / protein peptidyl-prolyl isomerization / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear matrix / SARS-CoV-1 activates/modulates innate immune responses / protein folding / nuclear speck ...cyclosporin A binding / protein peptidyl-prolyl isomerization / mRNA Splicing - Major Pathway / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nuclear matrix / SARS-CoV-1 activates/modulates innate immune responses / protein folding / nuclear speck / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) TOLYPOCLADIUM INFLATUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.75 Å | ||||||
Authors | Stegmann, C.M. / Sheldrick, G.M. / Wahl, M.C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009 Title: The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction. Authors: Stegmann, C.M. / Seeliger, D. / Sheldrick, G.M. / De Groot, B.L. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wfj.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfj.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfj ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
-Non-polymers , 4 types, 302 molecules
#3: Chemical | ChemComp-EDO / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. HERE, CYCLOSPORIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) ...CYCLOSPORI |
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Sequence details | INITIAL GA RESIDUES ARE CLONING ARTEFACTS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.4 % Description: STRUCTURE WAS SOLVED BY APPLYING DIRECT METHODS IN SHELXD IN TWO STAGES FIRST SEARCHING FOR 9 SULFUR ATOMS WITH THE HELP OF PATTERSON SEEDING AND DUAL-SPACE DIRECT METHODS AND THEN ...Description: STRUCTURE WAS SOLVED BY APPLYING DIRECT METHODS IN SHELXD IN TWO STAGES FIRST SEARCHING FOR 9 SULFUR ATOMS WITH THE HELP OF PATTERSON SEEDING AND DUAL-SPACE DIRECT METHODS AND THEN EXPANDING THE MOST PROMISING SOLUTIONS TO THE FULL STRUCTURE. DATA WERE COLLECTED FROM A SINGLE CRYSTAL FIRST ON A BRUKER ROTATING-ANODE GENERATOR, PRODUCING CUKALPHA RADIATION, AND A SMART6000 16-MEGAPIXEL CCD TO A RESOLUTION OF 1.12A. DATA FROM THE SAME CRYSTAL WERE THEN COLLECTED ON BEAMLINE PXII OF THE SWISS LIGHT SOURCE (SLS, VILLIGEN, SWITZERLAND) USING A MAR CCD 225 DETECTOR AND MERGED WITH THE IN-HOUSE DATA. |
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Crystal grow | pH: 8.5 Details: 28-32% (W/V) PEG 4000, 0.2M MGCL2, 0.1M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.6888 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: COLLIMATOR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6888 Å / Relative weight: 1 |
Reflection | Resolution: 0.75→40 Å / Num. obs: 212972 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.25 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 0.75→0.78 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.63 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: DIRECT METHODS Starting model: NONE Resolution: 0.75→10 Å / Num. parameters: 16518 / Num. restraintsaints: 21007 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 20 / Occupancy sum hydrogen: 1253.37 / Occupancy sum non hydrogen: 1660.65 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.75→10 Å
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Refine LS restraints |
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