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

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Basic information

Entry
Database: PDB / ID: 2iaa
TitleCrystal Structure of an Electron Transfer Complex Between Aromatic Amine Dephydrogenase and Azurin from Alcaligenes Faecalis (Form 2)
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 / MAD / Resolution: 1.95 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
DepositionSep 7, 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.
Remark 300BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 CHAIN(S). AUTHOR STATES THAT THE ASYMMETRIC UNIT CONTAINS ONE ALPHA-BETA-GAMMA HETEROTRIMER WHICH IS HALF THE BIOLOGICAL UNIT FOR A BINARY COMPLEX AND ONE ALPHA-BETA HETERODIMER WHICH IS NOT THE BIOLOGICAL ELECTRON TRANSFER BIOLOGICAL UNIT.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7666
Polymers128,7035
Non-polymers641
Water17,817989
1
A: Aromatic Amine Dehydrogenase
B: Aromatic Amine Dehydrogenase
C: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2714
Polymers71,2073
Non-polymers641
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-26 kcal/mol
Surface area24410 Å2
MethodPISA
2
D: Aromatic Amine Dehydrogenase
E: Aromatic Amine Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)57,4962
Polymers57,4962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-15 kcal/mol
Surface area19030 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-61 kcal/mol
Surface area38060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.216, 131.722, 133.204
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 / Fragment: residues 1-390 / 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 / Fragment: residues 1-135 / 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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 6
Details: PEG, MES and calcium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.381, 1.445
DetectorType: SBC / Detector: CCD / Date: Jun 7, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.3811
21.4451
ReflectionResolution: 1.95→47.04 Å / Num. all: 86390 / Num. obs: 80127 / % possible obs: 78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.8
Reflection shellHighest resolution: 1.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.4 / % possible all: 68.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.95→47.04 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 511838.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3893 5 %RANDOM
Rwork0.174 ---
obs0.174 77391 89.5 %-
all-86380 --
Displacement parametersBiso mean: 25.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.95→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8317 0 1 989 9307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
1.95-2.080.25325045.20.21588689140
2.08-2.240.2476200.204911743
2.24-2.460.23326140.187512386
2.46-2.820.22226990.180312783
2.82-3.550.19937030.162613459
3.55-47.040.1747530.159113987

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