[English] 日本語
Yorodumi- PDB-3rlm: Structure of the W199F MauG/pre-Methylamine Dehydrogenase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rlm | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the W199F MauG/pre-Methylamine Dehydrogenase complex after treatment with hydrogen peroxide | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / oxidoreductase | ||||||
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: 2.13 Å | ||||||
Authors | Yukl, E.T. / Wilmot, C.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Mutagenesis of tryptophan199 suggests that hopping is required for MauG-dependent tryptophan tryptophylquinone biosynthesis. Authors: Tarboush, N.A. / Jensen, L.M. / Yukl, E.T. / Geng, J. / Liu, A. / Wilmot, C.M. / Davidson, V.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3rlm.cif.gz | 683.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3rlm.ent.gz | 584.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rlm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rlm_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3rlm_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3rlm_validation.xml.gz | 72.5 KB | Display | |
Data in CIF | 3rlm_validation.cif.gz | 103.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/3rlm ftp://data.pdbj.org/pub/pdb/validation_reports/rl/3rlm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 41107.594 Da / Num. of mol.: 2 / Mutation: W199F 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4733 / Production host: Rhodobacter sphaeroides (bacteria) References: UniProt: A1BBA0, UniProt: P22619*PLUS, EC: 1.4.99.3 #3: Protein | Mass: 42449.277 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 sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3 |
---|
-Non-polymers , 5 types, 975 molecules
#4: Chemical | #5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-PGE / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1M MES, 0.1M sodium acetate, 23-25% w/v PEG 8000, 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-D / Wavelength: 1.03322 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2010 |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. all: 100983 / Num. obs: 95544 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 10.325 |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.111 / Rsym value: 0.347 / % possible all: 82.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→44.49 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.003 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.212 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.957 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→44.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.13→2.185 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|