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- PDB-2j55: X-ray reduced Paraccocus denitrificans methylamine dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 2j55
TitleX-ray reduced Paraccocus denitrificans methylamine dehydrogenase O- quinone in complex with amicyanin.
Components
  • (METHYLAMINE DEHYDROGENASE ...Amine dehydrogenase) x 2
  • AMICYANIN
KeywordsOXIDOREDUCTASE / TRANSPORT / PERIPLASMIC / METAL-BINDING / ELECTRON TRANSPORT / SINGLE CRYSTAL MICROSPECTROPHOTOMETRY
Function / homology
Function and homology information


methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / electron transfer activity / periplasmic space / 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 DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPearson, A.R. / Pahl, R. / Davidson, V.L. / Wilmot, C.M.
Citation
Journal: J.Synchrotron Radiat. / Year: 2007
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: Journal: To be Published
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
DepositionSep 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Data collection / Non-polymer description / Version format compliance
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 viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMICYANIN
B: AMICYANIN
H: METHYLAMINE DEHYDROGENASE HEAVY CHAIN
J: METHYLAMINE DEHYDROGENASE HEAVY CHAIN
L: METHYLAMINE DEHYDROGENASE LIGHT CHAIN
M: METHYLAMINE DEHYDROGENASE LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,82612
Polymers136,3306
Non-polymers4956
Water16,394910
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18040 Å2
ΔGint-67.3 kcal/mol
Surface area42000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.733, 122.733, 246.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / METHYLAMINE DEHYDROGENASE ... / Antibody , 3 types, 6 molecules ABHJLM

#1: Protein AMICYANIN /


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) PARACOCCUS DENITRIFICANS (bacteria) / References: UniProt: P22364
#2: Protein METHYLAMINE DEHYDROGENASE HEAVY CHAIN / Amine dehydrogenase / METHYLAMINE DEHYDROGENASE ALPHA CHAIN / MADH


Mass: 42449.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / References: UniProt: P29894, EC: 1.4.99.3
#3: Antibody METHYLAMINE DEHYDROGENASE LIGHT CHAIN / Amine dehydrogenase / METHYLAMINE DEHYDROGENASE BETA CHAIN / MADH


Mass: 14210.696 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / References: UniProt: P22619, EC: 1.4.99.3

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Non-polymers , 3 types, 916 molecules

#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAT 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, RESPECTIVELY. IN THIS ENTRY THE SEQUENCE ERRORS HAVE BEEN CORRECTED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growpH: 5.6 / Details: pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
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.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5081 5 %RANDOM
Rwork0.189 ---
obs0.192 96429 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9449 0 26 910 10385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0229763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.95413325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.53451225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85724.172453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.207151465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5591556
X-RAY DIFFRACTIONr_chiral_restr0.1540.21441
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027646
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.24869
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26275
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2899
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.56362
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94229869
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.02834024
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2714.53453
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 401
Rwork0.256 7004

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