+Open data
-Basic information
Entry | Database: PDB / ID: 4me2 | ||||||
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Title | Crystal Structure of THA8 protein from Brachypodium distachyon | ||||||
Components | Uncharacterized protein | ||||||
Keywords | RNA BINDING PROTEIN / Pentatricopeptide repeat protein / Helix-turn-helix repeats / Group II intron RNA binding / chloroplast | ||||||
Function / homology | Function and homology information Group II intron splicing / chloroplast organization / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Brachypodium distachyon (stiff brome) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Ke, J. / Chen, R.Z. / Ban, T. / Brunzelle, J.S. / Gu, X. / Melcher, K. / Xu, H.E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Structural basis for RNA recognition by a dimeric PPR-protein complex. Authors: Ke, J. / Chen, R.Z. / Ban, T. / Zhou, X.E. / Gu, X. / Tan, M.H. / Chen, C. / Kang, Y. / Brunzelle, J.S. / Zhu, J.K. / Melcher, K. / Xu, H.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4me2.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4me2.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 4me2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4me2_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 4me2_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 4me2_validation.xml.gz | 11 KB | Display | |
Data in CIF | 4me2_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/4me2 ftp://data.pdbj.org/pub/pdb/validation_reports/me/4me2 | HTTPS FTP |
-Related 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: 27752.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brachypodium distachyon (stiff brome) / Gene: BRADI2G00245, BRADI2G00270, THA8 / Plasmid: PET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I1HB13 |
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#2: 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: 1.75 Å3/Da / Density % sol: 29.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18% PEG 1500, 0.1 M HEPES, pH 7.5, 0.2 M L-Proline, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2013 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 25258 / Num. obs: 25258 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3660 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.286 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 28.301 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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