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Yorodumi- PDB-2wfi: Atomic resolution crystal structure of the PPIase domain of human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wfi | ||||||
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Title | Atomic resolution crystal structure of the PPIase domain of human cyclophilin G | ||||||
Components | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G | ||||||
Keywords | ISOMERASE / PHOSPHOPROTEIN / PRE-MRNA SPLICING / ALTERNATIVE SPLICING / NUCLEUS / ROTAMASE / CYCLOSPORIN / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE | ||||||
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 / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
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 | 2wfi.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfi.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfi ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfi | 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
#1: Protein | Mass: 19891.516 Da / Num. of mol.: 1 / Fragment: PPIASE DOMAIN, RESIDUES 1-177 Source method: isolated from a genetically manipulated source Details: CYS63 OXIDIZED TO CYSTEINE SULFONIC ACID / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA (DE3) (NOVAGEN) / References: UniProt: Q13427, peptidylprolyl isomerase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | 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: 1.93 Å3/Da / Density % sol: 36.1 % 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. |
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Crystal grow | pH: 8.5 Details: 28-32% PEG 4000 (W/V), 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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9 |
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: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.75→20 Å / Num. obs: 206194 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 7.15 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 0.75→0.76 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.68 / % possible all: 79.1 |
-Processing
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Refinement | Method to determine structure: DIRECT METHODS Starting model: NONE Resolution: 0.75→10 Å / Num. parameters: 17347 / Num. restraintsaints: 21296 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 30 / Occupancy sum hydrogen: 1274.41 / Occupancy sum non hydrogen: 1695.52 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.75→10 Å
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Refine LS restraints |
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