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- PDB-2iup: CRYSTAL STRUCTURE OF DITHIONITE-REDUCED AROMATIC AMINE DEHYDROGEN... -

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Basic information

Entry
Database: PDB / ID: 2iup
TitleCRYSTAL STRUCTURE OF DITHIONITE-REDUCED AROMATIC AMINE DEHYDROGENASE (AADH) FROM ALCALIGENES FAECALIS
Components
  • AROMATIC AMINE DEHYDROGENASE ALPHA SUBUNIT
  • AROMATIC AMINE DEHYDROGENASE BETA 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 ...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
Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesALCALIGENES FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsRoujeinikova, A. / Scrutton, N. / Leys, D.
CitationJournal: J. Biol. Chem. / Year: 2006
Title: Atomic level insight into the oxidative half-reaction of aromatic amine dehydrogenase.
Authors: Roujeinikova, A. / Scrutton, N.S. / Leys, D.
History
DepositionJun 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.temp
Revision 1.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AROMATIC AMINE DEHYDROGENASE ALPHA SUBUNIT
B: AROMATIC AMINE DEHYDROGENASE ALPHA SUBUNIT
D: AROMATIC AMINE DEHYDROGENASE BETA SUBUNIT
H: AROMATIC AMINE DEHYDROGENASE BETA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)109,0664
Polymers109,0664
Non-polymers00
Water21,1321173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.960, 89.063, 80.802
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997, 0.073, 0.02), (0.075, 0.941, 0.329), (0.005, 0.33, -0.944)
Vector: 0.06958, -0.0881, 0.55727)

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Components

#1: Protein AROMATIC AMINE DEHYDROGENASE ALPHA SUBUNIT


Mass: 40016.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ALCALIGENES FAECALIS (bacteria) / Strain: IFO 14479 / References: UniProt: P84888*PLUS, EC: 1.4.99.4
#2: Protein AROMATIC AMINE DEHYDROGENASE BETA SUBUNIT


Mass: 14516.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ALCALIGENES FAECALIS (bacteria) / Strain: IFO 14479 / References: UniProt: P84887*PLUS, EC: 1.4.99.4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE DATABASE REFERENCES FOR CHAIN A, B, D, H DO NOT CURRENTLY EXIST.

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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: 2.5 Å3/Da / Density % sol: 41 %
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
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 91209 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.1 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.179 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 4543 5 %RANDOM
Rwork0.147 ---
obs0.148 86487 98 %-
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: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0.94 Å2
2--0.01 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 0 1173 8508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217562
X-RAY DIFFRACTIONr_bond_other_d0.0020.026573
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.92510279
X-RAY DIFFRACTIONr_angle_other_deg0.693315339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5985947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53724.08348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.024151202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4281544
X-RAY DIFFRACTIONr_chiral_restr0.080.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021535
X-RAY DIFFRACTIONr_nbd_refined0.2020.21331
X-RAY DIFFRACTIONr_nbd_other0.2110.26723
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0970.23878
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2898
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4394.55999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.67467620
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.23893365
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.149122656
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.215 314
Rwork0.181 5943

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