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Yorodumi- PDB-7w5q: The Kruppel-associated box (KRAB) domain of human zinc finger pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w5q | ||||||
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Title | The Kruppel-associated box (KRAB) domain of human zinc finger protein 568 | ||||||
Components | Zinc finger protein 568 | ||||||
Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information embryonic placenta morphogenesis / Generic Transcription Pathway / in utero embryonic development / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Han, C.W. / Jang, S.B. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Structure of the kruppel-associated box (KRAB) domain Authors: Han, C.W. / Jang, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w5q.cif.gz | 125 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w5q.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 7w5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/7w5q ftp://data.pdbj.org/pub/pdb/validation_reports/w5/7w5q | HTTPS FTP |
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-Related structure data
Related structure data | 1v65S 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: 13940.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF568 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3ZCX4 |
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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: 4.8 Å3/Da / Density % sol: 74.37 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium formate dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→50 Å / Num. obs: 13618 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 60.85 Å2 / CC1/2: 0.895 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.61→2.66 Å / Num. unique obs: 576 / CC1/2: 0.094 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V65 Resolution: 2.73→41.89 Å / SU ML: 0.5015 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.4407 / Stereochemistry target values: CDL v1.2
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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 mean: 43.58 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.73→41.89 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.0292704609 Å / Origin y: -6.67902510344 Å / Origin z: 30.2667531724 Å
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Refinement TLS group | Selection details: all |