+Open data
-Basic information
Entry | Database: PDB / ID: 6eom | ||||||
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Title | Structure of DPP III from Caldithrix abyssi | ||||||
Components | MutT/NUDIX family protein | ||||||
Keywords | HYDROLASE / Caldithrix abyssi / Metallopeptidase / Dipeptidyl peptidase III / DPP III / Zinc-Hydrolase | ||||||
Function / homology | Peptidase family M49 / Peptidase family M49 / hydrolase activity / metal ion binding / ALANINE / LYSINE / MutT/NUDIX family protein Function and homology information | ||||||
Biological species | Caldithrix abyssi DSM 13497 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å | ||||||
Authors | Sabljic, I. | ||||||
Funding support | Croatia, 1items
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Citation | Journal: PLoS ONE / Year: 2018 Title: The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity. Authors: Sabljic, I. / Tomin, M. / Matovina, M. / Sucec, I. / Tomasic Paic, A. / Tomic, A. / Abramic, M. / Tomic, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eom.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eom.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 6eom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eom_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 6eom_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 6eom_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6eom_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/6eom ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eom | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65511.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldithrix abyssi DSM 13497 (bacteria) / Gene: Cabys_2252, Calab_3349 / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H1XW48 |
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-Non-polymers , 7 types, 342 molecules
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | ChemComp-CL / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-ALA / | #6: Chemical | ChemComp-LYS / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2705 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2014 | ||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2705 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→48 Å / Num. obs: 36965 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.042 / Rrim(I) all: 0.124 / Net I/σ(I): 13.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Se-Met labeled protein solved using MAD metode Resolution: 2.103→48 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.93 Å2 / Biso mean: 38.3051 Å2 / Biso min: 19.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.103→48 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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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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