+Open data
-Basic information
Entry | Database: PDB / ID: 7z35 | |||||||||
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Title | Crystal structure of PEX13 SH3 domain of Trypanosoma cruzi | |||||||||
Components | Putative peroxin 13 | |||||||||
Keywords | PROTEIN TRANSPORT / Peroxisomal protein import | |||||||||
Function / homology | Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Putative peroxin 13 Function and homology information | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Sonani, R.R. / Dubin, G. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: To Be Published Title: Crystal structure of PEX13 SH3 domain of Trypanosoma cruzi Authors: Sonani, R.R. / Dubin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z35.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z35.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z35_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 7z35_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 7z35_validation.xml.gz | 4 KB | Display | |
Data in CIF | 7z35_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/7z35 ftp://data.pdbj.org/pub/pdb/validation_reports/z3/7z35 | HTTPS FTP |
-Related structure data
Related structure data | 4afzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9004.163 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C4B63_4g75 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2VYH2 |
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#2: 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: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.8M Ammonium Sulphate, 0.1 Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.45 Å / Num. obs: 4552 / % possible obs: 99.58 % / Redundancy: 18 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.45 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 444 / CC1/2: 0.681 / % possible all: 99.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFZ Resolution: 2.3→45.45 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.937 / SU B: 18.316 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.44 Å2 / Biso min: 49.79 Å2
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Refinement step | Cycle: final / Resolution: 2.3→45.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.1493 Å / Origin y: 10.7583 Å / Origin z: 1.3912 Å
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