+Open data
-Basic information
Entry | Database: PDB / ID: 5iau | ||||||
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Title | A C69-family cysteine dipeptidase from Lactobacillus farciminis | ||||||
Components | Dipeptidase | ||||||
Keywords | HYDROLASE / C69 family / cysteine dipeptidase / Ntn hydrolase / Lactobacillus farciminis / Gly-Pro | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Lactobacillus farciminis KCTC 3681 = DSM 20184 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.781 Å | ||||||
Authors | Kono, R. / Watanabe, K. | ||||||
Citation | Journal: To Be Published Title: A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation Authors: Kono, R. / Watanabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iau.cif.gz | 510.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iau.ent.gz | 417.7 KB | Display | PDB format |
PDBx/mmJSON format | 5iau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/5iau ftp://data.pdbj.org/pub/pdb/validation_reports/ia/5iau | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 52904.344 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus farciminis KCTC 3681 = DSM 20184 (bacteria) Gene: FC68_GL001211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R1IQH8 #2: Chemical | ChemComp-EDO / #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: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.8 M 1,6-hexanediol, 10 mM CoCl2, 100 mM acetate (pH 4.8) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.781→38.877 Å / Num. obs: 254496 / % possible obs: 99.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 5.41 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.781→38.877 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.98 / 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: 1.781→38.877 Å
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Refine LS restraints |
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LS refinement shell |
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