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- PDB-2ojy: Crystal structure of indol-3-acetaldehyde derived TTQ-amide adduc... -

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Basic information

Entry
Database: PDB / ID: 2ojy
TitleCrystal structure of indol-3-acetaldehyde derived TTQ-amide adduct of aromatic amine dehydrogenase
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
2-(1H-INDOL-3-YL)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 / FOURIER SYNTHESIS / Resolution: 1.6 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 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)109,1226
Polymers108,7744
Non-polymers3482
Water21,3481185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-55 kcal/mol
Surface area31710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.890, 88.810, 80.390
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains biological heterotetramer

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Components

#1: Protein Aromatic amine dehydrogenase, small subunit


Mass: 14273.616 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: 40113.238 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-TSR / 2-(1H-INDOL-3-YL)ACETAMIDE


Mass: 174.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1185 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 1.98 % / Av σ(I) over netI: 7.6 / Number: 239366 / Rmerge(I) obs: 0.062 / Χ2: 0.87 / D res high: 1.6 Å / D res low: 29.8 Å / Num. obs: 115670 / % possible obs: 88.2
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.4529.893.20.0340.862.19637
2.743.4594.40.0450.832.04702
2.392.7489.30.0660.842699
2.172.3984.80.0870.872.01678
2.022.1784.50.1110.91.99829
1.92.02850.1550.911.971070
1.81.985.50.2180.91.951195
1.721.887.20.280.881.911344
1.661.7288.10.3380.861.881537
1.61.6689.70.3670.861.841657
ReflectionResolution: 1.6→30 Å / Num. obs: 115670 / % possible obs: 88 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.6
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.8 / % possible all: 90

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.926 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21201 5822 5 %RANDOM
Rwork0.17242 ---
obs0.17445 109712 88.2 %-
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: 22.289 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.31 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7341 0 26 1185 8552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0217631
X-RAY DIFFRACTIONr_bond_other_d0.0020.025104
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.94210371
X-RAY DIFFRACTIONr_angle_other_deg1.7863.00512373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71624.069349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.961151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4941544
X-RAY DIFFRACTIONr_chiral_restr0.1020.21118
X-RAY DIFFRACTIONr_gen_planes_refined00.028709
X-RAY DIFFRACTIONr_gen_planes_other00.021559
X-RAY DIFFRACTIONr_nbd_refined0.2160.21546
X-RAY DIFFRACTIONr_nbd_other0.2140.25831
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23729
X-RAY DIFFRACTIONr_nbtor_other0.1060.23906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2952
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2290.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9271.55052
X-RAY DIFFRACTIONr_mcbond_other0.2771.51945
X-RAY DIFFRACTIONr_mcangle_it1.2227650
X-RAY DIFFRACTIONr_scbond_it2.07733255
X-RAY DIFFRACTIONr_scangle_it2.8794.52721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 454 -
Rwork0.259 8191 -
obs--89.81 %

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