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Yorodumi- PDB-2nli: Crystal Structure of the complex between L-lactate oxidase and a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nli | |||||||||
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Title | Crystal Structure of the complex between L-lactate oxidase and a substrate analogue at 1.59 angstrom resolution | |||||||||
Components | Lactate oxidase | |||||||||
Keywords | OXIDOREDUCTASE / L-lactate oxidase / flavoenzyme / FMN / D-Lactate | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With oxygen as acceptor / FMN binding / oxidoreductase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Aerococcus viridans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | |||||||||
Authors | Furuichi, M. / Suzuki, N. / Balasundaresan, D. / Yoshida, Y. / Minagawa, H. / Watanabe, Y. / Kaneko, H. / Waga, I. / Kumar, P.K.R. / Mizuno, H. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: X-ray structures of Aerococcus viridans lactate oxidase and its complex with D-lactate at pH 4.5 show an alpha-hydroxyacid oxidation mechanism Authors: Furuichi, M. / Suzuki, N. / Dhakshnamoorhty, B. / Minagawa, H. / Yamagishi, R. / Watanabe, Y. / Goto, Y. / Kaneko, H. / Yoshida, Y. / Yagi, H. / Waga, I. / Kumar, P.K.R. / Mizuno, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nli.cif.gz | 160 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nli.ent.gz | 122.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/2nli ftp://data.pdbj.org/pub/pdb/validation_reports/nl/2nli | HTTPS FTP |
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-Related structure data
Related structure data | 2zfaC 1goxS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 40279.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aerococcus viridans (bacteria) / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q44467, lactate 2-monooxygenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE LIGAND, LAC, REPRESENTS D-LACTIC ACID. THE CHEMICAL COMPONENT DICTIONARY WILL BE RENAMED TO BE ...THE LIGAND, LAC, REPRESENTS | |
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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: 2.47 Å3/Da / Density % sol: 50.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2005 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. all: 103948 / Num. obs: 103948 / % possible obs: 98.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 5.8 % / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GOX Resolution: 1.59→41.89 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.488 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→41.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.63 Å / Total num. of bins used: 20
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