+Open data
-Basic information
Entry | Database: PDB / ID: 6xhz | ||||||
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Title | Alpha-lytic protease homolog N4 | ||||||
Components | N4: hypothetical protein | ||||||
Keywords | UNKNOWN FUNCTION / Pseudoprotease / trypsin-like fold | ||||||
Biological species | Streptomyces monomycini (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Nixon, C.F. / Marqusee, S.M. / Gee, C.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2021 Title: Exploring the Evolutionary History of Kinetic Stability in the alpha-Lytic Protease Family. Authors: Nixon, C.F. / Lim, S.A. / Sailer, Z.R. / Zheludev, I.N. / Gee, C.L. / Kelch, B.A. / Harms, M.J. / Marqusee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xhz.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xhz.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 6xhz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xhz_validation.pdf.gz | 415.6 KB | Display | wwPDB validaton report |
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Full document | 6xhz_full_validation.pdf.gz | 415.6 KB | Display | |
Data in XML | 6xhz_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 6xhz_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xhz ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xhz | HTTPS FTP |
-Related structure data
Related structure data | 3sgbS 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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Unit cell |
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-Components
#1: Protein | Mass: 21830.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces monomycini (bacteria) / Gene: hypothetical protein [Streptomyces monomycini]. / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)pLysS |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.93 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2019 |
Radiation | Monochromator: S111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→41.7 Å / Num. obs: 39417 / % possible obs: 86.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 11.303 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 625 / CC1/2: 0.278 / Rpim(I) all: 1.034 / Rrim(I) all: 1.462 / % possible all: 27.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SGB Resolution: 1.25→38.68 Å / SU ML: 0.1264 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8137 Stereochemistry target values: GeoStd + Monomer Library + 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: 19.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→38.68 Å
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Refine LS restraints |
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LS refinement shell |
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