+Open data
-Basic information
Entry | Database: PDB / ID: 1xx5 | ||||||
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Title | Crystal Structure of Natrin from Naja atra snake venom | ||||||
Components | Natrin 1 | ||||||
Keywords | TOXIN / Natrin / CRISPs / Naja atra | ||||||
Function / homology | Function and homology information calcium channel regulator activity / potassium channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Naja atra (Chinese cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wang, J. / Shen, B. / Lou, X.H. / Guo, M. / Teng, M.K. / Niu, L.W. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Blocking effect and crystal structure of natrin toxin, a cysteine-rich secretory protein from Naja atra venom that targets the BKCa channel Authors: Wang, J. / Shen, B. / Guo, M. / Lou, X.H. / Duan, Y. / Cheng, X.P. / Teng, M.K. / Niu, L.W. / Liu, Q. / Huang, Q. / Hao, Q. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Purification, partial characterization, crystallization and preliminary X-ray diffraction of two cysteine-rich secretory proteins from Naja atra and Trimeresurus stejnegeri venoms Authors: Tu, X. / Wang, J. / Guo, M. / Zheng, D. / Teng, M. / Niu, L. / Liu, Q. / Huang, Q. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xx5.cif.gz | 146.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xx5.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/1xx5 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/1xx5 | HTTPS FTP |
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-Related structure data
Related structure data | 1rc9S S: Starting model for refinement |
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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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24981.088 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: Q7T1K6 #2: Chemical | #3: 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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: NaCl, Tris-CL, EtOH, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9363 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9363 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 33482 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 47.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RC9 Resolution: 2.4→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 265136.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.6056 Å2 / ksol: 0.467293 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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