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

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Basic information

Entry
Database: PDB / ID: 1jmz
Titlecrystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida with inhibitor
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 / amine dehydrogenase activity / electron transfer activity / periplasmic space / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cytochrome c-like domain superfamily / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Few Secondary Structures / Irregular / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
HEME C / NICKEL (II) ION / P-NITROPHENYLHYDRAZINE / 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 / MOLECULAR REPLACEMENT / Resolution: 2 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

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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)103,3517
Polymers101,9023
Non-polymers1,4494
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-90 kcal/mol
Surface area32240 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)206,70114
Polymers203,8046
Non-polymers2,8988
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area25900 Å2
ΔGint-194 kcal/mol
Surface area61900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.21, 92.37, 79.30
Angle α, β, γ (deg.)90, 112.0, 90
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 , 4 types, 300 molecules

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


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


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-PND / P-NITROPHENYLHYDRAZINE


Mass: 153.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.78 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: Apr 25, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→34 Å / Num. obs: 75744 / % possible obs: 99.9 % / Observed criterion σ(F): 1
Reflection shellResolution: 2→2.09 Å / % possible all: 99.6
Reflection
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 3755 RANDOM
Rwork0.215 --
obs-74657 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7066 0 98 296 7460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.06
X-RAY DIFFRACTIONx_angle_deg1.638
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.211 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.009
LS refinement shell
*PLUS
Rfactor Rfree: 0.293 / Rfactor obs: 0.279

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