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- PDB-2h47: Crystal Structure of an Electron Transfer Complex Between Aromati... -

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Basic information

Entry
Database: PDB / ID: 2h47
TitleCrystal Structure of an Electron Transfer Complex Between Aromatic Amine Dephydrogenase and Azurin from Alcaligenes Faecalis (Form 1)
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 / : / 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 / : / Azurin / Quinoprotein amine dehydrogenase, beta chain-like / : / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / YVTN repeat-like/Quinoprotein amine dehydrogenase / Cupredoxin / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 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
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE SEQUENCE OF AROMATIC AMINE DEHYDROGENASE (CHAINS A,D,F,H,B,E,G,I) ARE NOT AVAILABLE AT ...SEQUENCE THE SEQUENCE OF AROMATIC AMINE DEHYDROGENASE (CHAINS A,D,F,H,B,E,G,I) ARE NOT AVAILABLE AT UNP SEQUENCE DATABASE AT THE TIME OF PROCESSING.
Remark 300BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 9 ...BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 9 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 AND THREE ALPHA-BETA HETERODIMERS, TWO OF WHICH FORM UNCOMPLEXED HETEROTETRAMER AND THE THIRD ASSOCIATES WITH THE HETEROTRIMER COMPLEX.

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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: Aromatic Amine Dehydrogenase
G: Aromatic Amine Dehydrogenase
H: Aromatic Amine Dehydrogenase
I: Aromatic Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,75810
Polymers243,6949
Non-polymers641
Water13,457747
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 area4120 Å2
ΔGint-29 kcal/mol
Surface area24890 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 area2680 Å2
ΔGint-15 kcal/mol
Surface area19770 Å2
MethodPISA
3
F: Aromatic Amine Dehydrogenase
G: 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 area2730 Å2
ΔGint-15 kcal/mol
Surface area19960 Å2
MethodPISA
4
H: Aromatic Amine Dehydrogenase
I: 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 area2740 Å2
ΔGint-16 kcal/mol
Surface area19910 Å2
MethodPISA
5
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
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-59 kcal/mol
Surface area38910 Å2
MethodPISA
6
F: Aromatic Amine Dehydrogenase
G: Aromatic Amine Dehydrogenase
H: Aromatic Amine Dehydrogenase
I: Aromatic Amine Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)114,9914
Polymers114,9914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-45 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.505, 124.612, 189.874
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.: 4 / 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.: 4 / 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.: 747 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 23-28% PEG 4000, 0.1M Tris and 0.2M sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 26, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 72744 / Num. obs: 50339 / % possible obs: 69.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2818 / % possible all: 39.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AH1

2ah1


Resolution: 2.6→34.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 605127.55 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5063 10.1 %RANDOM
Rwork0.188 ---
all-71840 --
obs-49958 69.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.2491 Å2 / ksol: 0.343646 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.2 Å20 Å20 Å2
2--8.37 Å20 Å2
3----1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16051 0 1 747 16799
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it3.32
X-RAY DIFFRACTIONc_scbond_it3.392
X-RAY DIFFRACTIONc_scangle_it4.632.5
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
2.6-2.760.344351310.20.256145314495
2.76-2.970.29857270.2226189
2.97-3.270.27867860.20777033
3.27-3.750.25918660.19857759
3.75-4.720.21079910.1589033
4.72-34.010.2283118010.20.177410386

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