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- PDB-2ah1: Crystal structure of aromatic amine dehydrogenase (AADH) from Alc... -

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Basic information

Entry
Database: PDB / ID: 2ah1
TitleCrystal structure of aromatic amine dehydrogenase (AADH) from Alcaligenes faecalis
Components(Aromatic amine dehydrogenase) x 2
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 / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.2 Å
AuthorsMasgrau, L. / Roujeinikova, A. / Johannissen, L.O. / Hothi, P. / Basran, J. / Ranaghan, K.E. / Mulholland, A.J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
CitationJournal: Science / Year: 2006
Title: Atomic description of an enzyme reaction dominated by proton tunneling
Authors: Masgrau, L. / Roujeinikova, A. / Johannissen, L.O. / Hothi, P. / Basran, J. / Ranaghan, K.E. / Mulholland, A.J. / Sutcliffe, M.J. / Scrutton, N.S. / Leys, D.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Aromatic amine dehydrogenase
H: Aromatic amine dehydrogenase
A: Aromatic amine dehydrogenase
B: Aromatic amine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)109,0664
Polymers109,0664
Non-polymers00
Water31,4181744
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-45 kcal/mol
Surface area31380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.777, 89.136, 80.324
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the biological unit (heterotetramer)

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Components

#1: Protein Aromatic amine dehydrogenase


Mass: 14516.898 Da / Num. of mol.: 2 / Fragment: residues 48-182 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P84887, EC: 1.4.99.4
#2: Protein Aromatic amine dehydrogenase


Mass: 40016.125 Da / Num. of mol.: 2 / Fragment: residues 73-433 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479
References: UniProt: Q0VKG7, UniProt: P84888*PLUS, EC: 1.4.99.4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1744 / 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: 2.4 Å3/Da / Density % sol: 47.03 %
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: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.2→15 Å / Num. obs: 288444 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.5
Reflection shellResolution: 1.2→1.25 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.2 / % possible all: 91

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.9999refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.2→12 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.469 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17 15336 5 %RANDOM
Rwork0.142 ---
all0.143 ---
obs0.143 288444 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: 14.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-1.58 Å2
2---0.68 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7258 0 0 1744 9002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217467
X-RAY DIFFRACTIONr_bond_other_d0.0010.026459
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.92410143
X-RAY DIFFRACTIONr_angle_other_deg0.945315081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2045935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82224.169343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.955151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0161541
X-RAY DIFFRACTIONr_chiral_restr0.1020.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028464
X-RAY DIFFRACTIONr_gen_planes_other00.021513
X-RAY DIFFRACTIONr_nbd_refined0.2040.21337
X-RAY DIFFRACTIONr_nbd_other0.2070.26797
X-RAY DIFFRACTIONr_nbtor_other0.0970.24035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.21312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.268
X-RAY DIFFRACTIONr_mcbond_it1.6311.55906
X-RAY DIFFRACTIONr_mcbond_other0.9541.51923
X-RAY DIFFRACTIONr_mcangle_it1.96527522
X-RAY DIFFRACTIONr_scbond_it2.92833322
X-RAY DIFFRACTIONr_scangle_it3.7124.52619
X-RAY DIFFRACTIONr_rigid_bond_restr1.346316870
X-RAY DIFFRACTIONr_sphericity_free15.36571744
X-RAY DIFFRACTIONr_sphericity_bonded7.057713725
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.258 1045
Rwork0.249 18806
all-19851

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