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- PDB-2h3x: Crystal Structure of an Electron Transfer Complex Between Aromati... -

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Basic information

Entry
Database: PDB / ID: 2h3x
TitleCrystal Structure of an Electron Transfer Complex Between Aromatic Amine Dehydrogenase and Azurin from Alcaligenes Faecalis (Form 3)
Components
  • (Aromatic Amine Dehydrogenase) x 2
  • Azurin
KeywordsOXIDOREDUCTASE/electron transport / Quinoprotein / tryptophan tryptophylquinone / cupredoxin / electron transfer / OXIDOREDUCTASE-electron transport COMPLEX
Function / homology
Function and homology information


aralkylamine dehydrogenase (azurin) / aralkylamine dehydrogenase (azurin) activity / aliphatic amine dehydrogenase activity / amine metabolic process / periplasmic space / electron transfer activity / copper ion binding
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 / Azurin ...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 / Azurin / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Azurin / Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSukumar, N. / Chen, Z. / Leys, D. / Scrutton, N.S. / Ferrati, D. / Merli, A. / Rossi, G.L. / Bellamy, H.D. / Chistoserdov, A. / Davidson, V.L. / Mathews, F.S.
Citation
Journal: Biochemistry / Year: 2006
Title: Crystal Structure of an Electron Transfer Complex between Aromatic Amine Dehydrogenase and Azurin from Alcaligenes faecalis.
Authors: Sukumar, N. / Chen, Z. / Ferrari, D. / Merli, A. / Rossi, G.L. / Bellamy, H.D. / Chistoserdov, A. / Davidson, V.L. / Mathews, F.S.
#1: Journal: 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
DepositionMay 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE THE SEQUENCE OF AROMATIC AMINE DEHYDROGENASE (CHAINS A,D,B,E) ARE NOT AVAILABLE AT UNP ...SEQUENCE THE SEQUENCE OF AROMATIC AMINE DEHYDROGENASE (CHAINS A,D,B,E) ARE NOT AVAILABLE AT UNP SEQUENCE DATABASE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aromatic Amine Dehydrogenase
B: Aromatic Amine Dehydrogenase
C: Azurin
D: Aromatic Amine Dehydrogenase
E: Aromatic Amine Dehydrogenase
F: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5418
Polymers142,4146
Non-polymers1272
Water11,728651
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-66 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.953, 94.762, 211.482
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: Protein Aromatic Amine Dehydrogenase


Mass: 42978.754 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
#2: Protein Aromatic Amine Dehydrogenase


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, EC: 1.4.99.4
#3: Protein Azurin


Mass: 13711.415 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P00281
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.26 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, Tris, potassium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 1.3753 Å
DetectorDetector: CCD / Date: Nov 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3753 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 45874 / Num. obs: 34130 / % possible obs: 74.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2794 / % possible all: 62.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3289 -RANDOM
Rwork0.183 ---
all-46065 --
obs-32934 71.5 %-
Displacement parametersBiso mean: 35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9433 0 2 651 10086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.660.32234090.2544X-RAY DIFFRACTION4001
2.66-2.870.27075650.2082X-RAY DIFFRACTION4839
2.87-3.150.25835270.184X-RAY DIFFRACTION5032
3.15-3.610.22155620.175X-RAY DIFFRACTION5055
3.61-4.550.20676010.1611X-RAY DIFFRACTION5098
4.55-47.790.20826250.184X-RAY DIFFRACTION5620

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