[English] 日本語
Yorodumi- PDB-4l3h: Crystal Structure of the E113Q-MauG/pre-Methylamine Dehydrogenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l3h | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the E113Q-MauG/pre-Methylamine Dehydrogenase Complex After Treatment with Hydrogen Peroxide | ||||||
Components |
| ||||||
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: 1.79 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4l3h.cif.gz | 724.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4l3h.ent.gz | 597.2 KB | Display | PDB format |
PDBx/mmJSON format | 4l3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l3h_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4l3h_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4l3h_validation.xml.gz | 81.8 KB | Display | |
Data in CIF | 4l3h_validation.cif.gz | 119.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/4l3h ftp://data.pdbj.org/pub/pdb/validation_reports/l3/4l3h | HTTPS FTP |
-Related structure data
Related structure data | 4l1qC 4l3gC 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: 41145.645 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: 15025.595 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 |
---|
-Non-polymers , 7 types, 1483 molecules
#4: Chemical | #5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | ChemComp-PGE / | #10: Water | ChemComp-HOH / | |
---|
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.94 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03313 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 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: 1.03313 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. all: 168632 / Num. obs: 162378 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.97 |
Reflection shell | Resolution: 1.79→1.82 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.17 / % possible all: 83.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3L4M Resolution: 1.79→44.49 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.765 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 39.525 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→44.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.79→1.836 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|