[English] 日本語
Yorodumi- PDB-3svw: Crystal Structure of the P107V-MauG/pre-Methylamine Dehydrogenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3svw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the P107V-MauG/pre-Methylamine Dehydrogenase Complex | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / MauG / methylamine dehydrogenase / c-heme / quinone cofactor / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Jensen, L.M.R. / Wilmot, C.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Proline 107 is a major determinant in maintaining the structure of the distal pocket and reactivity of the high-spin heme of MauG. Authors: Feng, M. / Jensen, L.M. / Yukl, E.T. / Wei, X. / Liu, A. / Wilmot, C.M. / Davidson, V.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3svw.cif.gz | 714.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3svw.ent.gz | 581.9 KB | Display | PDB format |
PDBx/mmJSON format | 3svw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3svw_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3svw_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3svw_validation.xml.gz | 86.5 KB | Display | |
Data in CIF | 3svw_validation.cif.gz | 130.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/3svw ftp://data.pdbj.org/pub/pdb/validation_reports/sv/3svw | HTTPS FTP |
-Related structure data
Related structure data | 3sjlC 3sleC 3l4mS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 41148.645 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 / Mutation: P107V 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: 15025.595 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188 Source method: isolated from a genetically manipulated source Details: Immature MADH (preMADH) was produced in the absence of the mauG gene. Trp57 is monohydroxylated at the C7 position. Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauA / Production host: Rhodobacter sphaeroides (bacteria) References: UniProt: P22619, UniProt: A1BBA0*PLUS, EC: 1.4.99.3 #3: Protein | Mass: 42449.277 Da / Num. of mol.: 2 / Fragment: UNP residues 32-417 Source method: isolated from a genetically manipulated source Details: Immature MADH (preMADH) was produced in the absence of the mauG gene. The alpha subunit has the wild-type sequence. Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4730 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3 |
---|
-Non-polymers , 9 types, 2126 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-HEC / #7: Chemical | ChemComp-PGE / | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-ACT / | #11: Chemical | ChemComp-MES / | #12: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM P107V-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 23% w/v PEG ...Details: Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM P107V-MauG and 50uM preMADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 23% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 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: 1.86→50 Å / Num. all: 149957 / Num. obs: 145458 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rsym value: 0.039 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.86→1.9 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 7.7 / Num. unique all: 7530 / Rsym value: 0.118 / % possible all: 86.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L4M Resolution: 1.86→33.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.965 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.366 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→33.89 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.862→1.91 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|