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- PDB-2j55: X-ray reduced Paraccocus denitrificans methylamine dehydrogenase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j55 | ||||||
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Title | X-ray reduced Paraccocus denitrificans methylamine dehydrogenase O- quinone in complex with amicyanin. | ||||||
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![]() | OXIDOREDUCTASE / TRANSPORT / PERIPLASMIC / METAL-BINDING / ELECTRON TRANSPORT / SINGLE CRYSTAL MICROSPECTROPHOTOMETRY | ||||||
Function / homology | ![]() methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pearson, A.R. / Pahl, R. / Davidson, V.L. / Wilmot, C.M. | ||||||
![]() | ![]() Title: Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry. Authors: Pearson, A.R. / Pahl, R. / Kovaleva, E.G. / Davidson, V.L. / Wilmot, C.M. #1: ![]() Title: Crystallographic Structures of Methylamine Dehydrogenase Catalytic Intermediates from Paraccocus Denitrificans Authors: De La Mora-Rey, T. / Pearson, A.R. / Hoeffner, E. / Watts, K.T. / Yucel, N. / Davidson, V.L. / Wilmot, C.M. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.5 KB | Display | ![]() |
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PDB format | ![]() | 214.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.1 KB | Display | ![]() |
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Full document | ![]() | 545.1 KB | Display | |
Data in XML | ![]() | 60.3 KB | Display | |
Data in CIF | ![]() | 86.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / METHYLAMINE DEHYDROGENASE ... / Antibody , 3 types, 6 molecules ABHJLM
#1: Protein | Mass: 11505.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: AMICYANIN IS THE OBLIGATE ELECTRON TRANSFER PARTNER OF METHYLAMINE DEHYDROGENASE. Source: (natural) ![]() #2: Protein | Mass: 42449.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Antibody | Mass: 14210.696 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 3 types, 916 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
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#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | AT PRESENT, THE SEQUENCE DATABASES INDICATE THAT RESIDUE 312 OF THE HEAVY CHAIN IS LEU AND RESIDUE ...AT PRESENT, THE SEQUENCE DATABASES INDICATE THAT RESIDUE 312 OF THE HEAVY CHAIN IS LEU AND RESIDUE 313 IS LEU. THE AUTHORS WHO DEPOSITED 2MTA FOUND THAT THEY MISREAD THE GELS AND THAT RESIDUES 312 AND 313 SHOULD BE PHE AND VAL, RESPECTIVE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.95 % |
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Crystal grow | pH: 5.6 / Details: pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→21.7 Å / Num. obs: 96429 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 59.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PRE-REDUCTION O-QUINONE FORM Resolution: 2.15→21.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.369 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.177 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→21.7 Å
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Refine LS restraints |
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