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Yorodumi- PDB-4zky: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zky | ||||||
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Title | Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis | ||||||
Components | Pyridoxamine 5-phosphate oxidase | ||||||
Keywords | OXIDOREDUCTASE / MSMEG_6526 / F420 / FDR / FDOR / FDR-B / Reductase | ||||||
Function / homology | Function and homology information F420-dependent enzyme, PPOX class, family Rv0121, probable / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Lee, B.M. / Carr, P.D. / Ahmed, F.H. / Jackson, C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. Authors: Ahmed, F.H. / Carr, P.D. / Lee, B.M. / Afriat-Jurnou, L. / Mohamed, A.E. / Hong, N.S. / Flanagan, J. / Taylor, M.C. / Greening, C. / Jackson, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zky.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zky.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4zky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/4zky ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zky | HTTPS FTP |
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-Related structure data
Related structure data | 4y9iC 4ybnC 5bncC 4qvbS 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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-Components
#1: Protein | Mass: 15839.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: L8F604, UniProt: A0R6F1*PLUS, pyridoxal 5'-phosphate synthase #2: Chemical | ChemComp-IOD / | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density % sol: 53.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Iodide, 22% Peg 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.81 Å / Num. obs: 39312 / % possible obs: 98.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.65→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 1.4 / % possible all: 76.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QVB Resolution: 1.65→19.396 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.396 Å
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Refine LS restraints |
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LS refinement shell |
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