+Open data
-Basic information
Entry | Database: PDB / ID: 2g4y | ||||||
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Title | structure of thaumatin at 2.0 A wavelength | ||||||
Components | Thaumatin-1 | ||||||
Keywords | PLANT PROTEIN / thaumatin structure at a wavelength of 2 A | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thaumatococcus daniellii (katemfe) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.98 Å | ||||||
Authors | Mueller-Dieckmann, C. / Weiss, M.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S. | ||||||
History |
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Remark 999 | SEQUENCE THERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM I IS USED BECAUSE THE ...SEQUENCE THERE ARE TWO ISOFORMS OF THAUMATION, I AND II. LYS46 FROM THE FORM I IS USED BECAUSE THE CRYSTALLIZATION MATERIAL CONTAINS A MIXTURE OF LYS AND ASN. ASP IS USED AT POSITION 113 AS SUGGESTED BY KO ET AL., ACTA CRYST. D50,813(1994) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4y.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4y.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 2g4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g4y_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 2g4y_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 2g4y_validation.xml.gz | 11 KB | Display | |
Data in CIF | 2g4y_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4y ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4y | HTTPS FTP |
-Related structure data
Related structure data | 2g4hC 2g4iC 2g4jC 2g4kC 2g4lC 2g4mC 2g4nC 2g4oC 2g4pC 2g4qC 2g4rC 2g4sC 2g4tC 2g4uC 2g4vC 2g4wC 2g4xC 2g4zC 2g51C 2g52C 2g55C 2illC C: citing same article (ref.) |
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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: 22243.119 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-TAR / |
#3: 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: 2.83 Å3/Da / Density % sol: 56.57 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→30 Å / Num. obs: 18622 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.378 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.031 Å / Total num. of bins used: 20
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