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- PDB-7ce5: Methanol-PQQ bound methanol dehydrogenase (MDH) from Methylococcu... -

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Basic information

Entry
Database: PDB / ID: 7ce5
TitleMethanol-PQQ bound methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath)
Components(Methanol dehydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / Methanol / PQQ
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c(L)) activity / 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
Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / 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 ...Methanol dehydrogenase, beta subunit / Methanol dehydrogenase, beta subunit superfamily / Methanol dehydrogenase beta subunit / 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 / Quinoprotein alcohol dehydrogenase-like superfamily
Similarity search - Domain/homology
METHANOL / PYRROLOQUINOLINE QUINONE / Methanol dehydrogenase [cytochrome c] subunit 2 / Methanol dehydrogenase protein, large subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChuankhayan, P. / Chan, S.I. / Nareddy, P.K.R. / Tsai, I.K. / Tsai, Y.F. / Chen, K.H.-C. / Yu, S.S.-F. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from Methylococcus capsulatus (Bath).
Authors: Chan, S.I. / Chuankhayan, P. / Reddy Nareddy, P.K. / Tsai, I.K. / Tsai, Y.F. / Chen, K.H. / Yu, S.S. / Chen, C.J.
History
DepositionJun 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methanol dehydrogenase protein, large subunit
B: Methanol dehydrogenase protein, large subunit
C: Methanol dehydrogenase protein, large subunit
D: Methanol dehydrogenase protein, large subunit
E: Methanol dehydrogenase [cytochrome c] subunit 2
F: Methanol dehydrogenase [cytochrome c] subunit 2
G: Methanol dehydrogenase protein, large subunit
H: Methanol dehydrogenase protein, large subunit
I: Methanol dehydrogenase [cytochrome c] subunit 2
J: Methanol dehydrogenase [cytochrome c] subunit 2
K: Methanol dehydrogenase [cytochrome c] subunit 2
L: Methanol dehydrogenase [cytochrome c] subunit 2
M: Methanol dehydrogenase protein, large subunit
N: Methanol dehydrogenase protein, large subunit
O: Methanol dehydrogenase [cytochrome c] subunit 2
P: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)578,56340
Polymers575,34416
Non-polymers3,21924
Water96,3805350
1
A: Methanol dehydrogenase protein, large subunit
E: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-45 kcal/mol
Surface area21340 Å2
MethodPISA
2
B: Methanol dehydrogenase protein, large subunit
F: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-43 kcal/mol
Surface area21400 Å2
MethodPISA
3
C: Methanol dehydrogenase protein, large subunit
K: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-43 kcal/mol
Surface area21450 Å2
MethodPISA
4
D: Methanol dehydrogenase protein, large subunit
L: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-44 kcal/mol
Surface area21450 Å2
MethodPISA
5
G: Methanol dehydrogenase protein, large subunit
I: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-46 kcal/mol
Surface area21320 Å2
MethodPISA
6
H: Methanol dehydrogenase protein, large subunit
J: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-43 kcal/mol
Surface area21450 Å2
MethodPISA
7
M: Methanol dehydrogenase protein, large subunit
O: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-43 kcal/mol
Surface area21230 Å2
MethodPISA
8
N: Methanol dehydrogenase protein, large subunit
P: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3205
Polymers71,9182
Non-polymers4023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-44 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.612, 211.828, 223.912
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Methanol dehydrogenase ... , 2 types, 16 molecules ABCDGHMNEFIJKLOP

#1: Protein
Methanol dehydrogenase protein, large subunit /


Mass: 63688.789 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath / References: UniProt: Q60AR6
#2: Protein
Methanol dehydrogenase [cytochrome c] subunit 2 / MDH small subunit beta / MDH-associated peptide / MEDH


Mass: 8229.256 Da / Num. of mol.: 8 / Source method: obtained synthetically
Source: (synth.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
References: UniProt: Q60AR3, methanol dehydrogenase (cytochrome c)

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Non-polymers , 4 types, 5374 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH4O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PQQ / PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone


Mass: 330.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5350 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 7.5 / Details: Hepes, PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→153 Å / Num. obs: 535098 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.9 / Net I/σ(I): 14.11
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 176635 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQO

4tqo


Resolution: 1.8→153 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17 27905 5 %RANDOM
Rwork0.14 ---
obs-507193 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40468 0 216 5350 46034
LS refinement shellResolution: 1.8→1.84 Å
RfactorNum. reflection% reflection
Rfree0.23 --
Rwork0.19 38966 -
obs-38966 98.81 %

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