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- PDB-7cfx: NAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus c... -

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Basic information

Entry
Database: PDB / ID: 7cfx
TitleNAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath)
Components
  • Methanol dehydrogenase [cytochrome c] subunit 2
  • Methanol dehydrogenase protein, large subunit
KeywordsOXIDOREDUCTASE / NAD / PQQ
Function / homology
Function and homology information


methanol dehydrogenase (cytochrome c) / methanol oxidation / alcohol dehydrogenase (cytochrome c(L)) activity / 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 / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Pyrrolo-quinoline quinone repeat / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily
Similarity search - Domain/homology
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: 2.5 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 29, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)578,30732
Polymers575,34416
Non-polymers2,96216
Water17,529973
1
C: Methanol dehydrogenase protein, large subunit
K: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-42 kcal/mol
Surface area21460 Å2
MethodPISA
2
D: Methanol dehydrogenase protein, large subunit
L: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-42 kcal/mol
Surface area21510 Å2
MethodPISA
3
A: Methanol dehydrogenase protein, large subunit
E: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-46 kcal/mol
Surface area21430 Å2
MethodPISA
4
B: Methanol dehydrogenase protein, large subunit
F: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-42 kcal/mol
Surface area21340 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)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-45 kcal/mol
Surface area21590 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)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-42 kcal/mol
Surface area21460 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)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-45 kcal/mol
Surface area21570 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)72,2884
Polymers71,9182
Non-polymers3702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-44 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.901, 211.028, 221.723
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#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: isolated from a natural source
Source: (natural) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria)
Strain: ATCC 33009 / NCIMB 11132 / Bath
References: UniProt: Q60AR3, methanol dehydrogenase (cytochrome c)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


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


Mass: 18.015 Da / Num. of mol.: 973 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 291 K / Method: microbatch / Details: Hepes, PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 195256 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 0.85 / CC star: 0.95 / Net I/σ(I): 13.5
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 26426 / Rpim(I) all: 0.34 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQO

4tqo


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24 --RANDOM0.178
Rwork0.18 ---
obs-195256 99 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40468 0 200 973 41641
LS refinement shellResolution: 2.5→2.56 Å
RfactorNum. reflection% reflection
Rfree0.29 -5 %
Rwork0.22 13990 -
obs--97.61 %

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