+Open data
-Basic information
Entry | Database: PDB / ID: 2hqx | ||||||
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Title | Crystal structure of human P100 tudor domain conserved region | ||||||
Components | P100 CO-ACTIVATOR TUDOR DOMAIN | ||||||
Keywords | TRANSCRIPTION / HUMAN P100 TUDOR DOMAIN / PROTEOLYTIC FRAGMENT / PSI / STRUCTURAL GENOMICS / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / Protein Structure Initiative / SECSG | ||||||
Function / homology | Function and homology information regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process ...regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process / RNA endonuclease activity / transcription coregulator activity / osteoblast differentiation / melanosome / Signaling by BRAF and RAF1 fusions / endonuclease activity / cadherin binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PT-SAS / Resolution: 1.42 Å | ||||||
Authors | Zhao, M. / Liu, Z.J. / Xu, H. / Yang, J. / Silvennoinen, O. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human P100 Tudor Domain Conserved Region Authors: Zhao, M. / Liu, Z.J. / Xu, H. / Yang, J. / Silvennoinen, O. / Wang, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hqx.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hqx.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/2hqx ftp://data.pdbj.org/pub/pdb/validation_reports/hq/2hqx | HTTPS FTP |
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-Related structure data
Related structure data | 2hqeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE INTACT P100 PROTEIN ASSOCIATES AS A DIMER |
-Components
#1: Protein | Mass: 27941.320 Da / Num. of mol.: 2 / Fragment: CONSERVED REGION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SND1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KZF4 #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 grow | Temperature: 291 K / Method: modified microbatch / pH: 7.9 Details: 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.0 MG/ML) AND RESERVOIR SOLUTION CONTAINING 1.06M AMMONIUM SULFATE, 200.0 MM LITHIUM SULFATE, 0.1M TRIS PH 7.9, ...Details: 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.0 MG/ML) AND RESERVOIR SOLUTION CONTAINING 1.06M AMMONIUM SULFATE, 200.0 MM LITHIUM SULFATE, 0.1M TRIS PH 7.9, MODIFIED MICROBATCH, temperature 291K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 25, 2005 / Details: ROSENBAUM | |||||||||
Radiation | Monochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.42→38.72 Å / Num. all: 27043 / Num. obs: 25303 / % possible obs: 82.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.05 / Net I/σ(I): 15.6 | |||||||||
Reflection shell | Resolution: 1.42→1.46 Å / Redundancy: 1.3 % / Num. unique all: 212 / Rsym value: 0.03 / % possible all: 23.08 |
-Processing
Software |
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Refinement | Method to determine structure: PT-SAS Starting model: PDB ENTRY 2HQE Resolution: 1.42→38.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 1.608 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→38.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.456 Å / Total num. of bins used: 20
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