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Yorodumi- PDB-5a30: Crystal structure of mtPAP N472D mutant in complex with ATPgammaS -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a30 | ||||||
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Title | Crystal structure of mtPAP N472D mutant in complex with ATPgammaS | ||||||
Components | MITOCHONDRIAL PROTEINMitochondrion | ||||||
Keywords | UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information histone mRNA catabolic process / poly(A) RNA polymerase activity / UTP binding / : / manganese ion binding / GTP binding / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Lapkouski, M. / Hallberg, B.M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structure of Mitochondrial Poly(A) RNA Polymerase Reveals the Structural Basis for Dimerization, ATP Selectivity and the Spax4 Disease Phenotype. Authors: Lapkouski, M. / Hallberg, B.M. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a30.cif.gz | 192.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a30.ent.gz | 155.9 KB | Display | PDB format |
PDBx/mmJSON format | 5a30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a30 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a30 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.4252, 0.8301, -0.3607), Vector: |
-Components
#1: Protein | Mass: 62955.078 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-568 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: F1NBW0 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | SINGLE POINT MUTATION N472D | |
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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: 2.17 Å3/Da / Density % sol: 43.3 % Description: RESOLUTION CUTOFF CRITERIA ACCORDING TO KARPLUS AND DIEDERICHS 2012 |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. obs: 29303 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.57 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.75→39.75 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.521 / SU ML: 0.359 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.509 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→39.75 Å
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Refine LS restraints |
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