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- PDB-2agy: Crystal structure of the Schiff base intermediate in the reductiv... -

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Basic information

Entry
Database: PDB / ID: 2agy
TitleCrystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with tryptamine. Monoclinic form
Components(Aromatic amine dehydrogenase) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


aralkylamine dehydrogenase (azurin) / aralkylamine dehydrogenase (azurin) activity / aliphatic amine dehydrogenase activity / amine metabolic process / periplasmic space
Similarity search - Function
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 / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase ...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 / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-(1H-INDOL-3-YL)ETHANIMINE / Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 Å
AuthorsMasgrau, L. / Roujeinikova, A. / Johannissen, L.O. / Hothi, P. / Basran, J. / Ranaghan, K.E. / Mulholland, A.J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
CitationJournal: Science / Year: 2006
Title: Atomic description of an enzyme reaction dominated by proton tunneling
Authors: Masgrau, L. / Roujeinikova, A. / Johannissen, L.O. / Hothi, P. / Basran, J. / Ranaghan, K.E. / Mulholland, A.J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Aromatic amine dehydrogenase
H: Aromatic amine dehydrogenase
A: Aromatic amine dehydrogenase
B: Aromatic amine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3826
Polymers109,0664
Non-polymers3162
Water27,2391512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-60 kcal/mol
Surface area31190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.703, 88.373, 79.709
Angle α, β, γ (deg.)90.00, 90.19, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the biological unit (heterotetramer)

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Components

#1: Protein Aromatic amine dehydrogenase


Mass: 14516.898 Da / Num. of mol.: 2 / Fragment: residues 48-182 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P84887, EC: 1.4.99.4
#2: Protein Aromatic amine dehydrogenase


Mass: 40016.125 Da / Num. of mol.: 2 / Fragment: residues 73-433 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P84888, EC: 1.4.99.4
#3: Chemical ChemComp-TSH / 2-(1H-INDOL-3-YL)ETHANIMINE


Mass: 158.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1512 / 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: 2.4 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 2000 MME, ammonium sulphate, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.1→15 Å / Num. obs: 357148 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.1
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 82

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.9999refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.1→15 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.152 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.163 18936 5 %RANDOM
Rwork0.144 ---
all0.144 ---
obs0.144 357148 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.49 Å2
2---0.4 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7245 0 24 1512 8781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217475
X-RAY DIFFRACTIONr_bond_other_d0.0010.026489
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9310152
X-RAY DIFFRACTIONr_angle_other_deg0.707315137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4915926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14924.064342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0711543
X-RAY DIFFRACTIONr_chiral_restr0.0930.21093
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028429
X-RAY DIFFRACTIONr_gen_planes_other00.021522
X-RAY DIFFRACTIONr_nbd_refined0.2050.21404
X-RAY DIFFRACTIONr_nbd_other0.2060.27102
X-RAY DIFFRACTIONr_nbtor_other0.1050.24192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.21203
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1070.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.280
X-RAY DIFFRACTIONr_mcbond_it1.5251.54853
X-RAY DIFFRACTIONr_mcbond_other1.0521.51919
X-RAY DIFFRACTIONr_mcangle_it1.94927497
X-RAY DIFFRACTIONr_scbond_it2.68433167
X-RAY DIFFRACTIONr_scangle_it3.4584.52655
X-RAY DIFFRACTIONr_rigid_bond_restr1.398315708
X-RAY DIFFRACTIONr_sphericity_free7.47331512
X-RAY DIFFRACTIONr_sphericity_bonded5.954313766
LS refinement shellResolution: 1.102→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.276 1284
Rwork0.251 25226
all-26510

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