+Open data
-Basic information
Entry | Database: PDB / ID: 7y39 | ||||||||||||
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Title | Ubiquitin-like domain of human ZFAND1 | ||||||||||||
Components | AN1-type zinc finger protein 1 | ||||||||||||
Keywords | PROTEIN BINDING / ZFAND1 / p97 / proteasome / stress granule / ubiquitin-like domain / proteostasis | ||||||||||||
Function / homology | Function and homology information positive regulation of intracellular protein transport / cellular response to arsenite ion / stress granule disassembly / proteasome binding / cytoplasmic stress granule / zinc ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å | ||||||||||||
Authors | Lai, C.H. / Ko, K.T. / Fan, P.J. / Yu, T.A. / Chang, C.F. / Draczkowski, P. / Hsu, S.T.D. | ||||||||||||
Funding support | Taiwan, 3items
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Citation | Journal: To Be Published Title: Structural Insight into ZFAND1 and p97 Interaction Authors: Lai, C.H. / Ko, K.T. / Fan, P.J. / Yu, T.A. / Chang, C.F. / Draczkowski, P. / Hsu, S.T.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y39.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y39.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 7y39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y39_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 7y39_full_validation.pdf.gz | 439.3 KB | Display | |
Data in XML | 7y39_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7y39_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/7y39 ftp://data.pdbj.org/pub/pdb/validation_reports/y3/7y39 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15679.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZFAND1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TCF1 #2: Water | ChemComp-HOH / | |
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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: 1.73 Å3/Da / Density % sol: 29.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES (pH6.5), 1.2M Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 22, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→30 Å / Num. obs: 17016 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.19 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.033 / Rrim(I) all: 0.059 / Χ2: 1.004 / Net I/σ(I): 12.5 / Num. measured all: 55773 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AF-Q8TCF1-F1 Resolution: 1.88→23.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.89 / 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: 73.76 Å2 / Biso mean: 28.1122 Å2 / Biso min: 13.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.88→23.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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