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- PDB-1jmx: crystal structure of a quinohemoprotein amine dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 1jmx
Titlecrystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida
Components(Amine Dehydrogenase) x 3
KeywordsOXIDOREDUCTASE / Amine Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With a copper protein as acceptor / aliphatic amine dehydrogenase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase, gamma subunit, structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, haem binding domain / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, beta subunit / Quinohemoprotein amine dehydrogenase, alpha subunit ...Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase, gamma subunit, structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, haem binding domain / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, beta subunit / Quinohemoprotein amine dehydrogenase, alpha subunit / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain superfamily / Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 superfamily / : / Quinohemoprotein amine dehydrogenase, gamma subunit / Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, alpha subunit domain II / : / Quinoprotein amine dehydrogenase, beta chain-like / Cytochrome c-like domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Lipocalin / Few Secondary Structures / Irregular / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HEME C / NICKEL (II) ION / Quinohemoprotein amine dehydrogenase subunit gamma / Quinohemoprotein amine dehydrogenase 40 kDa subunit / Quinohemoprotein amine dehydrogenase 60 kDa subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsSatoh, A. / Miyahara, I. / Hirotsu, K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges.
Authors: Satoh, A. / Kim, J.K. / Miyahara, I. / Devreese, B. / Vandenberghe, I. / Hacisalihoglu, A. / Okajima, T. / Kuroda, S. / Adachi, O. / Duine, J.A. / Van Beeumen, J. / Tanizawa, K. / Hirotsu, K.
History
DepositionJul 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amine Dehydrogenase
B: Amine Dehydrogenase
G: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1986
Polymers101,9023
Non-polymers1,2963
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-95 kcal/mol
Surface area32390 Å2
MethodPISA
2
A: Amine Dehydrogenase
B: Amine Dehydrogenase
G: Amine Dehydrogenase
hetero molecules

A: Amine Dehydrogenase
B: Amine Dehydrogenase
G: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,39512
Polymers203,8046
Non-polymers2,5916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area25070 Å2
ΔGint-203 kcal/mol
Surface area62200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.21, 92.37, 79.30
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABG

#1: Protein Amine Dehydrogenase


Mass: 53986.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8VW85
#2: Protein Amine Dehydrogenase


Mass: 39284.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8VW82
#3: Protein Amine Dehydrogenase


Mass: 8630.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: P0A182

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Non-polymers , 3 types, 460 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG MME2000, nickel chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
218 %(w/v)PEG2000 MME1reservoir
350 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 89255 / % possible obs: 99.9 % / Observed criterion σ(F): 2
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 3292 RANDOM
Rwork0.209 --
obs-64940 -
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7067 0 87 457 7611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.609
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.211 / Rfactor Rfree: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / Rfactor obs: 0.237

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