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Yorodumi- PDB-4l3g: Crystal Structure of the E113Q-MauG/pre-Methylamine Dehydrogenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l3g | ||||||
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Title | Crystal Structure of the E113Q-MauG/pre-Methylamine Dehydrogenase Complex Aged 120 Days | ||||||
Components |
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Keywords | OXIDOREDUCTASE / electron transfer | ||||||
Function / homology | Function and homology information methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity ...methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Yukl, E.T. / Wilmot, C.M. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Carboxyl Group of Glu113 Is Required for Stabilization of the Diferrous and Bis-Fe(IV) States of MauG. Authors: Abu Tarboush, N. / Yukl, E.T. / Shin, S. / Feng, M. / Wilmot, C.M. / Davidson, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l3g.cif.gz | 689.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l3g.ent.gz | 567.4 KB | Display | PDB format |
PDBx/mmJSON format | 4l3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l3g_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4l3g_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4l3g_validation.xml.gz | 73.5 KB | Display | |
Data in CIF | 4l3g_validation.cif.gz | 105.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/4l3g ftp://data.pdbj.org/pub/pdb/validation_reports/l3/4l3g | HTTPS FTP |
-Related structure data
Related structure data | 4l1qC 4l3hC 3l4mS C: citing same article (ref.) 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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-Components
-Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 41161.645 Da / Num. of mol.: 2 / Mutation: E113Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauG, Pden_4736 / Production host: Paracoccus denitrificans (bacteria) / References: UniProt: Q51658, Oxidoreductases #2: Antibody | Mass: 15039.577 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4733 / Production host: Rhodobacter spheroides (bacteria) / References: UniProt: A1BBA0, EC: 1.4.99.3 #3: Protein | Mass: 42321.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4730 / Production host: Rhodobacter spheroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3 |
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-Non-polymers , 6 types, 1076 molecules
#4: Chemical | #5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-NA / #7: Chemical | #8: Chemical | ChemComp-PGE / | #9: 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: 2.27 Å3/Da / Density % sol: 45.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1M MES pH 6.4, 0.1M sodium acetate, 24-30% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2011 / Details: BIOMORPH MIRRORS (KIRKPATRICK-BAEZ CONFIGURATION) |
Radiation | Monochromator: Si(111) Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 110057 / Num. obs: 107618 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.36 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.32 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3L4M Resolution: 2.05→29.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.237 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.168 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.576 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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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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