+Open data
-Basic information
Entry | Database: PDB / ID: 7elf | ||||||
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Title | Nitrilase-Like Protein Nit2 from Kluyve-romyces lactis | ||||||
Components | KLLA0E15247p | ||||||
Keywords | HYDROLASE / Nitrilase / Nit2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Kluyveromyces lactis (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Jin, C.W. / Chang, J.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Crystals / Year: 2021 Title: Crystal Structure of Nitrilase-Like Protein Nit2 from Kluyveromyces lactis. Authors: Jin, C.W. / Jin, H.S. / Jeong, B.C. / Cho, D.H. / Chun, H.S. / Kim, W.K. / Chang, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7elf.cif.gz | 458.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7elf.ent.gz | 377.2 KB | Display | PDB format |
PDBx/mmJSON format | 7elf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7elf_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 7elf_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 7elf_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 7elf_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/7elf ftp://data.pdbj.org/pub/pdb/validation_reports/el/7elf | HTTPS FTP |
-Related structure data
Related structure data | 4h5uS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33633.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_E15247g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CN52 #2: 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: 2.57 Å3/Da / Density % sol: 52.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 26% w/v polyethylene glycol (PEG 3350), 0.3M Ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 68559 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.991 / Net I/σ(I): 16.96 |
Reflection shell | Resolution: 2.2→2.28 Å / Num. unique obs: 6799 / CC1/2: 0.862 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H5U Resolution: 2.2→45.68 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.01 / 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: 2.2→45.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.7591 Å / Origin y: 5.2596 Å / Origin z: 20.527 Å
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Refinement TLS group | Selection details: all |