+Open data
-Basic information
Entry | Database: PDB / ID: 4zoh | ||||||||||||
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Title | Crystal structure of glyceraldehyde oxidoreductase | ||||||||||||
Components | (Putative oxidoreductase ...) x 3 | ||||||||||||
Keywords | OXIDOREDUCTASE / xanthine oxidoreductase family / molybdopterin cofactor / flavin adenine dinucleotide / iron-sulfur cluster | ||||||||||||
Function / homology | Function and homology information FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Nishimasu, H. / Fushinobu, S. / Wakagi, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Plos One / Year: 2016 Title: Archaeal Mo-Containing Glyceraldehyde Oxidoreductase Isozymes Exhibit Diverse Substrate Specificities through Unique Subunit Assemblies. Authors: Wakagi, T. / Nishimasu, H. / Miyake, M. / Fushinobu, S. #1: Journal: FEBS Lett. / Year: 2002 Title: A novel bifunctional molybdo-enzyme catalyzing both decarboxylation of indolepyruvate and oxidation of indoleacetaldehyde from a thermoacidophilic archaeon, Sulfolobus sp. strain 7. Authors: Wakagi, T. / Fukuda, E. / Ogawa, Y. / Kino, H. / Matsuzawa, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zoh.cif.gz | 258.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zoh.ent.gz | 199.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zoh_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4zoh_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4zoh_validation.xml.gz | 49.4 KB | Display | |
Data in CIF | 4zoh_validation.cif.gz | 70.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/4zoh ftp://data.pdbj.org/pub/pdb/validation_reports/zo/4zoh | HTTPS FTP |
-Related structure data
Related structure data | 1ffvS S: Starting model for refinement |
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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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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
-Components
-Putative oxidoreductase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 77852.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea) Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / References: UniProt: Q96Y29 |
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#2: Protein | Mass: 30752.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea) Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / References: UniProt: Q974U9 |
#3: Protein | Mass: 18643.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea) Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / References: UniProt: Q974V0 |
-Non-polymers , 9 types, 633 molecules
#4: Chemical | ChemComp-MCN / | ||||||||||
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#5: Chemical | ChemComp-MO / | ||||||||||
#6: Chemical | ChemComp-1PE / | ||||||||||
#7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-FAD / | #9: Chemical | ChemComp-PG4 / | #10: Chemical | ChemComp-ACY / | #11: Chemical | #12: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % / Description: hexagonal pillar |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 MNa-acetate, 0.2M CH3COONH4, 15% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 2, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 73074 / % possible obs: 100 % / Redundancy: 12.1 % / Rsym value: 0.078 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 6.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FFV Resolution: 2.2→41.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.419 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.736 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→41.4 Å
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