+Open data
-Basic information
Entry | Database: PDB / ID: 4zxr | ||||||
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Title | Structure of Thaumatin wrapped in graphene within vacuum | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / Thaumatin / vacuum / graphene / graphene-wrapped protein crystals | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Aller, P. / Warren, A.J. / Trincao, J. / Evans, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: In vacuo X-ray data collection from graphene-wrapped protein crystals. Authors: Warren, A.J. / Crawshaw, A.D. / Trincao, J. / Aller, P. / Alcock, S. / Nistea, I. / Salgado, P.S. / Evans, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zxr.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zxr.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/4zxr ftp://data.pdbj.org/pub/pdb/validation_reports/zx/4zxr | HTTPS FTP |
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-Related structure data
Related structure data | 1kwn 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
#1: Protein | Mass: 22227.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thaumatococcus daniellii (katemfe) / References: UniProt: P02883 | ||
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#2: Chemical | ChemComp-TLA / | ||
#3: Chemical | #4: 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: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: Commercial thaumatin from Thaumatococcus danielli (Sigma-Aldrich) was resuspended in Milli-Q water to a concentration of 40 mg/mL. Sitting drops were made by mixing 4 uL of protein solution ...Details: Commercial thaumatin from Thaumatococcus danielli (Sigma-Aldrich) was resuspended in Milli-Q water to a concentration of 40 mg/mL. Sitting drops were made by mixing 4 uL of protein solution and 2 uL of reservoir solution [50 mM N-(2-Acetamido)iminodiacetic acid(ADA) pH 6.8, 600 mM potassium sodium tartrate and 20 % (v/v) Glycerol] and equilibrated against 500 uL of reservoir solution at 293K. |
-Data collection
Diffraction | Mean temperature: 295 K Ambient temp details: sample wrapped in graphene whithin low vacuum in vacuum chamber | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: double crystals Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.92→41.78 Å / Num. obs: 20125 / % possible obs: 95.9 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 10.6 / Num. measured all: 73107 / Scaling rejects: 21 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KWN 1kwn Resolution: 1.92→41.78 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1713 / WRfactor Rwork: 0.145 / FOM work R set: 0.8698 / SU B: 5.934 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1048 / SU Rfree: 0.1017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.69 Å2 / Biso mean: 37.326 Å2 / Biso min: 21.83 Å2
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Refinement step | Cycle: final / Resolution: 1.92→41.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.2885 Å / Origin y: 24.8265 Å / Origin z: 32.6369 Å
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