+Open data
-Basic information
Entry | Database: PDB / ID: 4tzm | ||||||
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Title | C. elegans HTP-2 bound to HTP-3 closure motif 1 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / HORMA domain / Meiosis / Chromosome axis | ||||||
Function / homology | Function and homology information meiotic DNA double-strand break formation / regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / condensed chromosome / chromosome / chromatin Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rosenberg, S.C. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Dev.Cell / Year: 2014 Title: The Chromosome Axis Controls Meiotic Events through a Hierarchical Assembly of HORMA Domain Proteins. Authors: Kim, Y. / Rosenberg, S.C. / Kugel, C.L. / Kostow, N. / Rog, O. / Davydov, V. / Su, T.Y. / Dernburg, A.F. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tzm.cif.gz | 212.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tzm.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 4tzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/4tzm ftp://data.pdbj.org/pub/pdb/validation_reports/tz/4tzm | HTTPS FTP |
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-Related structure data
Related structure data | 4trkC 4tzjC 4tzlSC 4tznC 4tzoC 4tzqC 4tzsC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 28744.303 Da / Num. of mol.: 2 / Fragment: UNP residues 1-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: htp-2, CELE_Y73B6BL.2, Y73B6BL.2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q95XC8 #2: Protein/peptide | Mass: 1796.038 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: HTP-3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: O01820*PLUS #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 15-22% PEG 3350 / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 24989 / % possible obs: 93.8 % / Redundancy: 3.3 % / Rsym value: 0.087 / Net I/σ(I): 14.5 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TZL Resolution: 2.3→28.465 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.35 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→28.465 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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