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- PDB-3c75: Paracoccus versutus methylamine dehydrogenase in complex with ami... -

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Basic information

Entry
Database: PDB / ID: 3c75
TitleParacoccus versutus methylamine dehydrogenase in complex with amicyanin
Components
  • Amicyanin
  • Methylamine dehydrogenase heavy chain
  • Methylamine dehydrogenase light chain
KeywordsOXIDOREDUCTASE / copper proteins / electron transfer complex / TTQ / Electron transport / Periplasm / Transport / Metal-binding / Pyrrolidone carboxylic acid
Function / homology
Function and homology information


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
Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) ...Amicyanin, Paracoccus/Methylobacterium / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Amicyanin/Pseudoazurin / Quinoprotein amine dehydrogenase, beta chain-like / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Amicyanin / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesParacoccus versutus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCavalieri, C. / Biermann, N. / Vlasie, M.D. / Einsle, O. / Merli, A. / Ferrari, D. / Rossi, G.L. / Ubbink, M.
CitationJournal: Biochemistry / Year: 2008
Title: Structural comparison of crystal and solution states of the 138 kDa complex of methylamine dehydrogenase and amicyanin from Paracoccus versutus.
Authors: Cavalieri, C. / Biermann, N. / Vlasie, M.D. / Einsle, O. / Merli, A. / Ferrari, D. / Rossi, G.L. / Ubbink, M.
History
DepositionFeb 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Methylamine dehydrogenase heavy chain
L: Methylamine dehydrogenase light chain
A: Amicyanin
J: Methylamine dehydrogenase heavy chain
M: Methylamine dehydrogenase light chain
B: Amicyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,3558
Polymers162,2286
Non-polymers1272
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16290 Å2
ΔGint-71.6 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.573, 131.038, 171.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Methylamine dehydrogenase heavy chain / MADH


Mass: 46430.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus versutus (bacteria) / References: UniProt: P23006, EC: 1.4.99.3
#2: Antibody Methylamine dehydrogenase light chain / MADH / Methylamine dehydrogenase subunit beta


Mass: 20409.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus versutus (bacteria) / References: UniProt: P22641, EC: 1.4.99.3
#3: Protein Amicyanin


Mass: 14273.489 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus versutus (bacteria) / References: UniProt: P22365
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 293 K / pH: 6.5
Details: PEG 8000; lithium sulfate, phosphate buffer, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.8414
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 8, 2005 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8414 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 37332 / % possible obs: 84.1 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.51
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.25 / % possible all: 80.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.15 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1130 -RANDOM
Rwork0.235 ---
obs0.235 35392 82.4 %-
all-44390 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.53 Å20 Å20 Å2
2---6.918 Å20 Å2
3---22.448 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9408 0 2 393 9803
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1731.5
X-RAY DIFFRACTIONc_mcangle_it1.9722
X-RAY DIFFRACTIONc_scbond_it1.6672
X-RAY DIFFRACTIONc_scangle_it2.452.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4copper.par

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