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Yorodumi- PDB-4lk8: Crystal structure of CyaY protein from Psychromonas ingrahamii in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lk8 | ||||||
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Title | Crystal structure of CyaY protein from Psychromonas ingrahamii in complex with Co(II) | ||||||
Components | Protein CyaY | ||||||
Keywords | METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Psychromonas ingrahamii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å | ||||||
Authors | Noguera, M.E. / Roman, E.A. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2015 Title: Structural characterization of metal binding to a cold-adapted frataxin Authors: Noguera, M.E. / Roman, E.A. / Rigal, J.B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lk8.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lk8.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 4lk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/4lk8 ftp://data.pdbj.org/pub/pdb/validation_reports/lk/4lk8 | HTTPS FTP |
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-Related structure data
Related structure data | 4lp1C 4hs5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 105 / Label seq-ID: 1 - 105
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-Components
#1: Protein | Mass: 12295.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: cyaY, Ping_0042 / Plasmid: pJexpress411:56977 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A1SR01 #2: Chemical | ChemComp-CO / #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: 1.9 Å3/Da / Density % sol: 35.23 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 20mM sodium acetate, 200mM MgCl2, 29.5% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91907 Å | |||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2012 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91907 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.494→30.425 Å / Num. all: 53634 / Num. obs: 53634 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.61 Å2 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HS5 Resolution: 1.494→30.425 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 23.5 / Stereochemistry target values: ML Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED 2. THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS UNDER F_PLUS/MINUS COLUMNS.
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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 max: 70.75 Å2 / Biso mean: 27.8952 Å2 / Biso min: 12.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.494→30.425 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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