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Yorodumi- PDB-4a0h: Structure of bifunctional DAPA aminotransferase-DTB synthetase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a0h | ||||||
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Title | Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana bound to 7-keto 8-amino pelargonic acid (KAPA) | ||||||
Components | ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / BIO3-BIO1 / BIOTIN SYNTHESIS | ||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / dethiobiotin synthase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / magnesium ion binding / protein homodimerization activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.808 Å | ||||||
Authors | Cobessi, D. / Dumas, R. / Pautre, V. / Meinguet, C. / Ferrer, J.L. / Alban, C. | ||||||
Citation | Journal: Plant Cell / Year: 2012 Title: Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis. Authors: Cobessi, D. / Dumas, R. / Pautre, V. / Meinguet, C. / Ferrer, J.L. / Alban, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a0h.cif.gz | 584.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a0h.ent.gz | 479.3 KB | Display | PDB format |
PDBx/mmJSON format | 4a0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a0h_validation.pdf.gz | 506.3 KB | Display | wwPDB validaton report |
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Full document | 4a0h_full_validation.pdf.gz | 567.1 KB | Display | |
Data in XML | 4a0h_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 4a0h_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a0h ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a0h | HTTPS FTP |
-Related structure data
Related structure data | 4a0fSC 4a0gC 4a0rC S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.695211, -0.09778, -0.712124), Vector: |
-Components
#1: Protein | Mass: 91427.188 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-833 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B0F481 #2: Chemical | #3: Chemical | ChemComp-KAP / #4: Chemical | |
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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 Å3/Da / Density % sol: 39.3 % / Description: NONE |
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Crystal grow | Details: 0.2 M AMMONIUM TARTRATE PH 6.2, 15 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979701 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DOUBLE SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979701 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→44.57 Å / Num. obs: 36581 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Biso Wilson estimate: 52.68 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.22 |
Reflection shell | Resolution: 2.81→2.88 Å / Redundancy: 1.74 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.61 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4A0F Resolution: 2.808→44.572 Å / SU ML: 0.74 / σ(F): 1.99 / Phase error: 29.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.332 Å2 / ksol: 0.331 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.808→44.572 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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