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- PDB-2ok6: Crystal structure of aromatic amine dehydrogenase TTQ-formamide a... -

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Basic information

Entry
Database: PDB / ID: 2ok6
TitleCrystal structure of aromatic amine dehydrogenase TTQ-formamide adduct oxidized with ferricyanide.
Components
  • Aromatic amine dehydrogenase, large subunit
  • Aromatic amine dehydrogenase, small subunit
KeywordsOXIDOREDUCTASE / TTQ
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 ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
BENZOIC ACID / 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: 1.45 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
DepositionJan 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)109,3086
Polymers109,0644
Non-polymers2442
Water30,3551685
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11280 Å2
ΔGint-33 kcal/mol
Surface area31570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.338, 89.266, 80.494
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains a biological heterotetramer

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Components

#1: Protein Aromatic amine dehydrogenase, small subunit


Mass: 14515.914 Da / Num. of mol.: 2 / Fragment: (Residues: 48-182) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria)
References: UniProt: Q0VKG6, UniProt: P84887*PLUS, EC: 1.4.99.4
#2: Protein Aromatic amine dehydrogenase, large subunit


Mass: 40016.125 Da / Num. of mol.: 2 / Fragment: (Residues: 73-433) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria)
References: UniProt: Q0VKG7, UniProt: P84888*PLUS, EC: 1.4.99.4
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1685 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.89 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.45 Å / Num. obs: 161574

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.249 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19172 8526 5 %RANDOM
Rwork0.16086 ---
obs0.16242 161574 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: 15.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0.87 Å2
2---0.15 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7377 0 16 1685 9078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217659
X-RAY DIFFRACTIONr_bond_other_d0.0010.026605
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.93410416
X-RAY DIFFRACTIONr_angle_other_deg0.834315427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0895959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87324.148352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.323151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5161542
X-RAY DIFFRACTIONr_chiral_restr0.0970.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.028722
X-RAY DIFFRACTIONr_gen_planes_other00.021554
X-RAY DIFFRACTIONr_nbd_refined0.2060.21459
X-RAY DIFFRACTIONr_nbd_other0.1960.27307
X-RAY DIFFRACTIONr_nbtor_refined0.180.23758
X-RAY DIFFRACTIONr_nbtor_other0.090.24455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21356
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9644.54808
X-RAY DIFFRACTIONr_mcbond_other0.7014.51950
X-RAY DIFFRACTIONr_mcangle_it2.49867662
X-RAY DIFFRACTIONr_scbond_it3.65593239
X-RAY DIFFRACTIONr_scangle_it5.207122750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.454→1.492 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 525 -
Rwork0.266 9758 -
obs--100 %

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