+Open data
-Basic information
Entry | Database: PDB / ID: 5lxz | ||||||
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Title | W288A mutant of GlxA from Streptomyces lividans: Cu-bound form | ||||||
Components | Secreted proteinSecretory protein | ||||||
Keywords | TRANSPORT PROTEIN / copper / metalloradical / AA5 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces lividans TK24 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Chaplin, A.K. / Hough, M.A. / Worrall, J.A.R. | ||||||
Citation | Journal: to be published Title: The role of a second-coordination sphere tryptophan residue in the maturation of the catalytic metalloradical site in the auxillary activity family 5 (AA5) GlxA from Streptomyces lividans Authors: Chaplin, A.K. / Svistunenko, D.A. / Hough, M.A. / Wilson, M.T. / Vijgenboom, E. / Worrall, J.A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lxz.cif.gz | 155.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lxz.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/5lxz ftp://data.pdbj.org/pub/pdb/validation_reports/lx/5lxz | HTTPS FTP |
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-Related structure data
Related structure data | 4unmS 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
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 66048.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans TK24 (bacteria) / Gene: SLIV_23470 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6EWM0 |
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-Non-polymers , 5 types, 681 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: 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: 3.04 Å3/Da / Density % sol: 59.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% PEG 20000, 0.1M sodium acetate pH 5 15 mg/ml protein |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2015 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→40.48 Å / Num. obs: 130534 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Rrim(I) all: 0.106 / Net I/σ(I): 7.6 / Num. measured all: 480382 / Scaling rejects: 351 |
Reflection shell | Resolution: 1.49→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2 / CC1/2: 0.616 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4unm Resolution: 1.49→40.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.117 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0578 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.058 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.78 Å2 / Biso mean: 14.632 Å2 / Biso min: 5.03 Å2
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Refinement step | Cycle: final / Resolution: 1.49→40.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.49→1.529 Å / Total num. of bins used: 20
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