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Yorodumi- PDB-3pxs: Crystal Structure of Diferrous MauG in Complex with Pre-Methylami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pxs | ||||||
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Title | Crystal Structure of Diferrous MauG in Complex with Pre-Methylamine Dehydrogenase: | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / Oxidoreductase / electron transport / periplasmic space / 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: 2.22 Å | ||||||
Authors | Yukl, E.T. / Goblirsch, B.R. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Crystal Structures of CO and NO Adducts of MauG in Complex with Pre-Methylamine Dehydrogenase: Implications for the Mechanism of Dioxygen Activation. Authors: Yukl, E.T. / Goblirsch, B.R. / Davidson, V.L. / Wilmot, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pxs.cif.gz | 657 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pxs.ent.gz | 560.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pxs_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 3pxs_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3pxs_validation.xml.gz | 71.5 KB | Display | |
Data in CIF | 3pxs_validation.cif.gz | 102.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/3pxs ftp://data.pdbj.org/pub/pdb/validation_reports/px/3pxs | HTTPS FTP |
-Related 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: 41146.629 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 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: mauA / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22619, 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 Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauB / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3 |
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-Non-polymers , 7 types, 1066 molecules
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-HEC / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PG4 / | #9: Chemical | ChemComp-PG6 / | #10: 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: 45.87 % |
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Crystal grow | Temperature: 293 K / pH: 6.4 Details: 0.1M MES pH 6.4, 0.1M sodium acetate, 23-25 % w/v PEG 8000, vapor diffusion, hanging drop, temperature 293K , VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2010 / 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: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→50 Å / Num. obs: 83223 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 27.15 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.865 |
Reflection shell | Resolution: 2.22→2.26 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.061 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→44.49 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.03 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→44.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.28 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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