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- PDB-2i0r: Crystal structure of aromatic amine dehydrogenase TTQ-formamide adduct -

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Basic information

Entry
Database: PDB / ID: 2i0r
TitleCrystal structure of aromatic amine dehydrogenase TTQ-formamide adduct
Components(Aromatic Amine Dehydrogenase) x 2
KeywordsOXIDOREDUCTASE / TTQ / carbinolamine oxidation
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
Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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
DepositionAug 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...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 / struct_conn
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.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
Remark 999SEQUENCE Database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)107,4004
Polymers107,4004
Non-polymers00
Water30,6261700
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-42 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.662, 88.415, 80.034
Angle α, β, γ (deg.)90.000, 90.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aromatic Amine Dehydrogenase


Mass: 13742.205 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
#2: Protein Aromatic Amine Dehydrogenase


Mass: 39958.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P84888, EC: 1.4.99.4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1700 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 2000 MME, AMMONIUM SULPHATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. obs: 192659 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.3 / Num. measured all: 100020 / Num. unique all: 28110 / Rsym value: 0.311 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.802 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.165 9682 5 %RANDOM
Rwork0.139 ---
all0.14 192630 --
obs-192630 99.85 %-
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: 9.901 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.37 Å2
2--0.09 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7478 0 0 1700 9178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227678
X-RAY DIFFRACTIONr_bond_other_d0.0020.026632
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.93710440
X-RAY DIFFRACTIONr_angle_other_deg0.826315486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025965
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41724.314357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.292151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8321542
X-RAY DIFFRACTIONr_chiral_restr0.0930.21128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021543
X-RAY DIFFRACTIONr_nbd_refined0.2090.21445
X-RAY DIFFRACTIONr_nbd_other0.1980.27320
X-RAY DIFFRACTIONr_nbtor_refined0.180.23837
X-RAY DIFFRACTIONr_nbtor_other0.0980.24656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21349
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.287
X-RAY DIFFRACTIONr_mcbond_it0.8311.54864
X-RAY DIFFRACTIONr_mcbond_other0.2181.51977
X-RAY DIFFRACTIONr_mcangle_it1.31627744
X-RAY DIFFRACTIONr_scbond_it2.06733144
X-RAY DIFFRACTIONr_scangle_it3.1274.52694
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 709 -
Rwork0.2 13413 -
obs-14122 99.89 %

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