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- PDB-2i0s: Crystal structure of aromatic amine dehydrogenase TTQ-phenylaceta... -

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Basic information

Entry
Database: PDB / ID: 2i0s
TitleCrystal structure of aromatic amine dehydrogenase TTQ-phenylacetaldehyde adduct
Components(Aromatic amine dehydrogenaseAralkylamine dehydrogenase (azurin)) x 2
KeywordsOXIDOREDUCTASE / TTQ / carbinolamine oxidation
Function / homology
Function and homology information


aralkylamine dehydrogenase (azurin) / aralkylamine dehydrogenase (azurin) activity / 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
PHENYLACETALDEHYDE / Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsRoujeinikova, A. / Leys, D.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: New insights into the reductive half-reaction mechanism of aromatic amine dehydrogenase revealed by reaction with carbinolamine substrates.
Authors: Roujeinikova, A. / Hothi, P. / Masgrau, L. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
History
DepositionAug 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE Database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)107,3876
Polymers107,1464
Non-polymers2402
Water31,4001743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-36 kcal/mol
Surface area32250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.619, 88.821, 79.942
Angle α, β, γ (deg.)90.000, 90.560, 90.000
Int Tables number4
Space group name H-MP1211
Detailsthe asymmetric unit contains the biological heterotetramer

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Components

#1: Protein Aromatic amine dehydrogenase / Aralkylamine dehydrogenase (azurin)


Mass: 13714.194 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / References: UniProt: P84887*PLUS, EC: 1.4.99.4
#2: Protein Aromatic amine dehydrogenase / Aralkylamine dehydrogenase (azurin)


Mass: 39858.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / References: UniProt: P84888, EC: 1.4.99.4
#3: Chemical ChemComp-HY1 / PHENYLACETALDEHYDE / Phenylacetaldehyde


Mass: 120.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1743 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG2000 MME, Ammonium Sulphate, Sodium Cocadylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→44.412 Å / Num. obs: 192803 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 4.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.2 / Num. measured all: 97454 / Num. unique all: 27965 / Rsym value: 0.321 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.814 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 9711 5 %RANDOM
Rwork0.145 ---
all0.147 192688 --
obs-192688 99.59 %-
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: 10.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å2-0.31 Å2
2--0.26 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7478 0 18 1743 9239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227706
X-RAY DIFFRACTIONr_bond_other_d0.0010.026635
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9410478
X-RAY DIFFRACTIONr_angle_other_deg0.81315501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0355966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69124.354356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.271151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7131541
X-RAY DIFFRACTIONr_chiral_restr0.0880.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021542
X-RAY DIFFRACTIONr_nbd_refined0.2070.21419
X-RAY DIFFRACTIONr_nbd_other0.1950.27351
X-RAY DIFFRACTIONr_nbtor_refined0.180.23800
X-RAY DIFFRACTIONr_nbtor_other0.0970.24573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.21367
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.278
X-RAY DIFFRACTIONr_mcbond_it0.891.55017
X-RAY DIFFRACTIONr_mcbond_other0.2141.51978
X-RAY DIFFRACTIONr_mcangle_it1.22427753
X-RAY DIFFRACTIONr_scbond_it1.97833201
X-RAY DIFFRACTIONr_scangle_it2.694.52709
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 762 -
Rwork0.193 13276 -
obs-14038 98.75 %

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