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- PDB-2q7q: Crystal structure of Alcaligenes faecalis AADH in complex with p-... -

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Basic information

Entry
Database: PDB / ID: 2q7q
TitleCrystal structure of Alcaligenes faecalis AADH in complex with p-chlorobenzylamine.
Components
  • Aralkylamine dehydrogenase heavy chain
  • Aralkylamine dehydrogenase light chain
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 / 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
1-(4-CHLOROPHENYL)METHANAMINE / Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsRoujeinikova, A. / Leys, D.
CitationJournal: Biochemistry / Year: 2007
Title: Isotope effects reveal that para-substituted benzylamines are poor reactivity probes of the quinoprotein mechanism for aromatic amine dehydrogenase.
Authors: Hothi, P. / Roujeinikova, A. / Khadra, K.A. / Lee, M. / Cullis, P. / Leys, D. / Scrutton, N.S.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Aralkylamine dehydrogenase light chain
H: Aralkylamine dehydrogenase light chain
A: Aralkylamine dehydrogenase heavy chain
B: Aralkylamine dehydrogenase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7386
Polymers107,4554
Non-polymers2832
Water21,9781220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-63 kcal/mol
Surface area31970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.541, 96.762, 120.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Aralkylamine dehydrogenase light chain / Aromatic amine dehydrogenase / AADH


Mass: 13713.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aauA / Production host: Escherichia coli (E. coli) / References: UniProt: P84887, EC: 1.4.99.4
#2: Protein Aralkylamine dehydrogenase heavy chain / Aromatic amine dehydrogenase / AADH


Mass: 40014.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aauB / Production host: Escherichia coli (E. coli) / References: UniProt: P84888, EC: 1.4.99.4
#3: Chemical ChemComp-C2B / 1-(4-CHLOROPHENYL)METHANAMINE


Mass: 141.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8ClN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1220 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
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

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 135347 / % possible obs: 95.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Χ2: 1.03 / Net I/σ(I): 20.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.663.10.454124561.278188.8
1.66-1.723.10.338126331.251190
1.72-1.83.10.242131181.171193
1.8-1.93.10.179133711.152195.3
1.9-2.023.20.127136311.062196.7
2.02-2.173.20.099138041.1197.9
2.17-2.393.30.088139230.87198.2
2.39-2.743.30.079140100.973198.6
2.74-3.453.30.071140950.872198.4
3.45-303.30.07143060.698197

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.676 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 6757 5 %RANDOM
Rwork0.165 ---
obs0.166 134278 95.51 %-
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: 20.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7326 0 18 1220 8564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227548
X-RAY DIFFRACTIONr_bond_other_d0.0010.026539
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.93610257
X-RAY DIFFRACTIONr_angle_other_deg0.815315263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79124.121347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.828151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6021543
X-RAY DIFFRACTIONr_chiral_restr0.0870.21108
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021524
X-RAY DIFFRACTIONr_nbd_refined0.2190.21331
X-RAY DIFFRACTIONr_nbd_other0.1890.26954
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23642
X-RAY DIFFRACTIONr_nbtor_other0.0930.24322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2896
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.257
X-RAY DIFFRACTIONr_mcbond_it2.0934.54773
X-RAY DIFFRACTIONr_mcbond_other0.7244.51931
X-RAY DIFFRACTIONr_mcangle_it2.87367580
X-RAY DIFFRACTIONr_scbond_it4.05593140
X-RAY DIFFRACTIONr_scangle_it5.9122679
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 418 -
Rwork0.242 8655 -
obs-9073 88.73 %

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