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- PDB-3w20: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygena... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w20 | ||||||
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Title | Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | OXIDOREDUCTASE / DSBH fold / Dioxygenase / Zn / alpha-KG binding | ||||||
Function / homology | q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Prolyl 4-hydroxylase alpha subunit Fe(2+) 2OG dioxygenase domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qin, H.M. / Miyakawa, T. / Jia, M.Z. / Nakamura, A. / Ohtsuka, J. / Xue, Y.L. / Kawashima, T. / Kasahara, T. / Hibi, M. / Ogawa, J. / Tanokura, M. | ||||||
![]() | ![]() Title: Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD Authors: Qin, H.M. / Miyakawa, T. / Jia, M.Z. / Nakamura, A. / Ohtsuka, J. / Xue, Y.L. / Kawashima, T. / Kasahara, T. / Hibi, M. / Ogawa, J. / Tanokura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 90.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.6 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31172.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES, 30%(w/v) PEG3000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 51288 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rsym value: 0.066 / Net I/σ(I): 68.2 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 10.5 % / Num. unique all: 2448 / Rsym value: 0.317 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE SEMET SUBSTITUTES OF SADA WAS USED AS A STARTING MODEL. 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: 25.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.813 Å / Total num. of bins used: 20
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