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- PDB-2hkr: Structures of the carbinolamine and schiff-base intermediates in ... -

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Basic information

Entry
Database: PDB / ID: 2hkr
TitleStructures of the carbinolamine and schiff-base intermediates in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with p-methoxyphenylethylamine
Components
  • Aromatic amine dehydrogenase, large subunit
  • Aromatic amine dehydrogenase, small subunit
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-(4-METHOXYPHENYL)ETHANAMINE / 2-(4-METHOXYPHENYL)ACETAMIDE / Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain / 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: To be Published
Title: Structure-reactivity correlations and kinetic isotope effects in aromatic amine dehydrogenase
Authors: Hothi, P. / Roujeinikova, A. / Sutcliffe, M.J. / Cullis, P. / Leys, D. / Scrutton, N.S.
History
DepositionJul 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Aromatic amine dehydrogenase, small subunit
H: Aromatic amine dehydrogenase, small subunit
A: Aromatic amine dehydrogenase, large subunit
B: Aromatic amine dehydrogenase, large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4836
Polymers107,1664
Non-polymers3162
Water24,9151383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-53 kcal/mol
Surface area31760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.848, 88.813, 80.044
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe asymmetric unit contains the biological heterotetramer (alpha)2(beta)2

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Components

#1: Protein Aromatic amine dehydrogenase, small subunit


Mass: 13469.881 Da / Num. of mol.: 2 / Fragment: AADH, small subunit, (residues 59-180) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479
References: UniProt: Q0VKG6, UniProt: P84887*PLUS, EC: 1.4.99.4
#2: Protein Aromatic amine dehydrogenase, large subunit


Mass: 40113.238 Da / Num. of mol.: 2 / Fragment: AADH, large subunit, (residues 4-364)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aauB / Production host: Escherichia coli (E. coli)
References: UniProt: Q0VKG7, UniProt: P84888*PLUS, EC: 1.4.99.4
#3: Chemical ChemComp-ZHH / 2-(4-METHOXYPHENYL)ETHANAMINE


Mass: 151.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO
#4: Chemical ChemComp-ZHZ / 2-(4-METHOXYPHENYL)ACETAMIDE


Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1383 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
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: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 189477

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.863 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 9510 5 %RANDOM
Rwork0.149 ---
all0.151 ---
obs-189392 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: 13.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.5 Å2
2---0.13 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7360 0 23 1383 8766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227728
X-RAY DIFFRACTIONr_bond_other_d0.0010.026707
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.94110526
X-RAY DIFFRACTIONr_angle_other_deg0.758315681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33224.143350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.696151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5571543
X-RAY DIFFRACTIONr_chiral_restr0.0820.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021559
X-RAY DIFFRACTIONr_nbd_refined0.2140.21350
X-RAY DIFFRACTIONr_nbd_other0.1960.27136
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23761
X-RAY DIFFRACTIONr_nbtor_other0.0980.24424
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21052
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.251
X-RAY DIFFRACTIONr_mcbond_it1.84.54948
X-RAY DIFFRACTIONr_mcbond_other0.5384.51980
X-RAY DIFFRACTIONr_mcangle_it2.15767792
X-RAY DIFFRACTIONr_scbond_it3.33993215
X-RAY DIFFRACTIONr_scangle_it4.691122726
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 646 -
Rwork0.239 12246 -
obs-12892 100 %

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