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- PDB-2oiz: Crystal Structure of the Tryptamine-Derived (Indol-3-Acetamide)-T... -

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Basic information

Entry
Database: PDB / ID: 2oiz
TitleCrystal Structure of the Tryptamine-Derived (Indol-3-Acetamide)-TTQ Adduct of Aromatic Amine Dehydrogenase
Components
  • Aromatic amine dehydrogenase, large subunit
  • Aromatic amine dehydrogenase, small subunit
KeywordsOXIDOREDUCTASE / tryptophan tryptophyl quinone / H-tunneling
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)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: 1.05 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 12, 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 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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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)109,6097
Polymers109,0664
Non-polymers5433
Water29,2741625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-51 kcal/mol
Surface area32340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.944, 88.705, 80.222
Angle α, β, γ (deg.)90.00, 90.36, 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: 14516.898 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-TSR / 2-(1H-INDOL-3-YL)ACETAMIDE


Mass: 174.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1625 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 2000 MME, AMMONIUM SULPHATE, SODIUM CACODYLATE, TRYPTAMINE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: TRIANGULAR HORIZONTAL- FOCUSING SI III MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.05→15 Å / Num. obs: 383635 / % possible obs: 83.6 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.064 / Χ2: 0.954 / Net I/σ(I): 16.5
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 1.9 / Num. unique all: 16727 / Χ2: 1.056 / % possible all: 73

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0011refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.05→15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.69 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.141 19254 5 %RANDOM
Rwork0.117 ---
obs0.118 365027 83.43 %-
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: 11.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.85 Å2
2---0.33 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 39 1625 9035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217885
X-RAY DIFFRACTIONr_bond_other_d0.0020.026836
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.94210740
X-RAY DIFFRACTIONr_angle_other_deg1.085315984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91724.028355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.506151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4071545
X-RAY DIFFRACTIONr_chiral_restr0.1110.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028999
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021615
X-RAY DIFFRACTIONr_nbd_refined0.2090.21390
X-RAY DIFFRACTIONr_nbd_other0.2040.27163
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23819
X-RAY DIFFRACTIONr_nbtor_other0.0940.24180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.21212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5090.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.286
X-RAY DIFFRACTIONr_mcbond_it2.6064.55149
X-RAY DIFFRACTIONr_mcbond_other2.5374.52005
X-RAY DIFFRACTIONr_mcangle_it3.00267910
X-RAY DIFFRACTIONr_scbond_it3.9993390
X-RAY DIFFRACTIONr_scangle_it5.016122815
X-RAY DIFFRACTIONr_rigid_bond_restr1.929316706
X-RAY DIFFRACTIONr_sphericity_free8.08931626
X-RAY DIFFRACTIONr_sphericity_bonded4.723314488
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 1263 -
Rwork0.21 23539 -
obs-24802 73.17 %

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