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- PDB-2d0v: Crystal structure of methanol dehydrogenase from Hyphomicrobium d... -

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Basic information

Entry
Database: PDB / ID: 2d0v
TitleCrystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans
Components
  • methanol dehydrogenase large subunit
  • methanol dehydrogenase small subunit
KeywordsOXIDOREDUCTASE / electron transfer / calcium binding / methanol / PQQ
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c(L)) activity => GO:0052933 / alcohol dehydrogenase (cytochrome c(L)) activity => GO:0052933 / alcohol dehydrogenase (cytochrome c(L)) activity => GO:0052933 / methanol dehydrogenase (cytochrome c) / methanol oxidation / oxidoreductase activity, acting on CH-OH group of donors / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / calcium ion binding / membrane
Similarity search - Function
Bacterial quinoprotein dehydrogenases signature 1. / Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family ...Bacterial quinoprotein dehydrogenases signature 1. / Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / PQQ enzyme repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 8 Propeller / Methanol Dehydrogenase; Chain A / Quinoprotein alcohol dehydrogenase-like superfamily / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Methanol dehydrogenase [cytochrome c] subunit 2 / Methanol dehydrogenase large subunit
Similarity search - Component
Biological speciesHyphomicrobium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsNojiri, M. / Hira, D. / Yamaguchi, K. / Suzuki, S.
CitationJournal: Biochemistry / Year: 2006
Title: Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins
Authors: Nojiri, M. / Hira, D. / Yamaguchi, K. / Okajima, T. / Tanizawa, K. / Suzuki, S.
History
DepositionAug 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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: methanol dehydrogenase large subunit
B: methanol dehydrogenase small subunit
D: methanol dehydrogenase large subunit
E: methanol dehydrogenase small subunit
I: methanol dehydrogenase large subunit
J: methanol dehydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,75512
Polymers223,6446
Non-polymers1,1116
Water13,097727
1
A: methanol dehydrogenase large subunit
B: methanol dehydrogenase small subunit
hetero molecules

A: methanol dehydrogenase large subunit
B: methanol dehydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8378
Polymers149,0964
Non-polymers7414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
2
D: methanol dehydrogenase large subunit
E: methanol dehydrogenase small subunit
I: methanol dehydrogenase large subunit
J: methanol dehydrogenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8378
Polymers149,0964
Non-polymers7414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-77 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)291.320, 63.999, 109.941
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1028-

HOH

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Components

#1: Protein methanol dehydrogenase large subunit


Mass: 66173.641 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hyphomicrobium denitrificans (bacteria) / Strain: A3151 / References: UniProt: Q4AE26, EC: 1.1.99.8
#2: Protein methanol dehydrogenase small subunit


Mass: 8374.417 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hyphomicrobium denitrificans (bacteria) / Strain: A3151 / References: UniProt: Q4AE23, EC: 1.1.99.8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H6N2O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.2 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 19, 2005
RadiationMonochromator: double crystals Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.49→44.6 Å / Num. all: 68299 / Num. obs: 68299 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→44.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.094 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24687 6898 10.1 %RANDOM
Rwork0.14863 ---
all0.192 68299 --
obs0.15854 61400 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.61 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å20 Å2-0.97 Å2
2--2.47 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.49→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15689 0 75 727 16491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02116230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3281.93722065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.10551991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06624.828783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.191152544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561557
X-RAY DIFFRACTIONr_chiral_restr0.1620.22223
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212770
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.28447
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.210807
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.21131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1351.510137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.874215784
X-RAY DIFFRACTIONr_scbond_it3.01437471
X-RAY DIFFRACTIONr_scangle_it4.4284.56281
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.493→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 472 -
Rwork0.195 4325 -
obs--95.48 %

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