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- PDB-1jju: Structure of a Quinohemoprotein Amine Dehydrogenase with a Unique... -

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Basic information

Entry
Database: PDB / ID: 1jju
TitleStructure of a Quinohemoprotein Amine Dehydrogenase with a Unique Redox Cofactor and Highly Unusual Crosslinking
Components(QUINOHEMOPROTEIN AMINE ...) x 3
KeywordsELECTRON TRANSPORT PROTEIN / QUINOHEMOPROTEIN / AMINE DEHYDROGENASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With a cytochrome as acceptor / oxidoreductase activity, acting on the CH-NH2 group of donors / 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / TERTIARY-BUTYL ALCOHOL / Quinohemoprotein amine dehydrogenase 40 kDa subunit / Quinohemoprotein amine dehydrogenase subunit gamma / Quinohemoprotein amine dehydrogenase 60 kDa subunit
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.05 Å
AuthorsDatta, S. / Mori, Y. / Takagi, K. / Kawaguchi, K. / Chen, Z.-W. / Kano, K. / Ikeda, T. / Okajima, T. / Kuroda, S. / Tanizawa, K. / Mathews, F.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking.
Authors: Datta, S. / Mori, Y. / Takagi, K. / Kawaguchi, K. / Chen, Z.W. / Okajima, T. / Kuroda, S. / Ikeda, T. / Kano, K. / Tanizawa, K. / Mathews, F.S.
History
DepositionJul 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: 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: QUINOHEMOPROTEIN AMINE DEHYDROGENASE
B: QUINOHEMOPROTEIN AMINE DEHYDROGENASE
C: QUINOHEMOPROTEIN AMINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9799
Polymers98,5013
Non-polymers1,4786
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-96 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.489, 99.489, 214.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsMolecule is heterotrimer in solution

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Components

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QUINOHEMOPROTEIN AMINE ... , 3 types, 3 molecules ABC

#1: Protein QUINOHEMOPROTEIN AMINE DEHYDROGENASE


Mass: 52711.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / Strain: IFO12442 / References: UniProt: Q8VUT0
#2: Protein QUINOHEMOPROTEIN AMINE DEHYDROGENASE


Mass: 37021.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / Strain: IFO12442 / References: UniProt: Q8VUS7
#3: Protein QUINOHEMOPROTEIN AMINE DEHYDROGENASE


Mass: 8767.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / Strain: IFO12442 / References: UniProt: Q8VUS8

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Non-polymers , 4 types, 641 molecules

#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, tert-butanol, citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
3100 mMsodium citrate1reservoirpH5.6
418 %PEG40001reservoir
521 %t-butyl alcohol1reservoir

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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: Oct 21, 1999 / Details: mirrors
RadiationMonochromator: MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 68364 / Num. obs: 58964 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 24.9
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2850 / % possible all: 50.6
Reflection
*PLUS
Highest resolution: 2.04 Å
Reflection shell
*PLUS
% possible obs: 50.6 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.05→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 5993 -RANDOM
Rwork0.202 ---
all-68364 --
obs-58964 86.4 %-
Solvent computationBsol: 48.6423 Å2 / ksol: 0.32865 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 87 650 7698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.379 649 -
Rwork0.348 --
obs-5650 56.2 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.6 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.379 / Rfactor Rwork: 0.348

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