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- PDB-4tqo: The crystal structure of methanol dehydrogenase from Methylococcu... -

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Basic information

Entry
Database: PDB / ID: 4tqo
TitleThe crystal structure of methanol dehydrogenase from Methylococcus capsulatus (Bath)
Components
  • Methanol dehydrogenase protein, large subunit
  • Methanol dehydrogenase, small subunit
KeywordsOXIDOREDUCTASE / dimer / 8-fold core propeller fold
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; 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 ...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 protein, large subunit
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsCulpepper, M.A. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Protein-Protein Interactions of Methanol Dehydrogenase from Methylococcus capsulatus (Bath).
Authors: Culpepper, M.A. / Rosenzweig, A.C.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 22, 2014Group: Database references
Revision 1.3Dec 4, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)578,30732
Polymers575,34416
Non-polymers2,96216
Water42,3712352
1
B: Methanol dehydrogenase protein, large subunit
I: Methanol dehydrogenase, small subunit
G: Methanol dehydrogenase protein, large subunit
O: Methanol dehydrogenase, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5778
Polymers143,8364
Non-polymers7414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-89 kcal/mol
Surface area39840 Å2
MethodPISA
2
A: Methanol dehydrogenase protein, large subunit
J: Methanol dehydrogenase, small subunit
E: Methanol dehydrogenase protein, large subunit
M: Methanol dehydrogenase, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5778
Polymers143,8364
Non-polymers7414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-90 kcal/mol
Surface area39890 Å2
MethodPISA
3
C: Methanol dehydrogenase protein, large subunit
K: Methanol dehydrogenase, small subunit
D: Methanol dehydrogenase protein, large subunit
L: Methanol dehydrogenase, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5778
Polymers143,8364
Non-polymers7414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-90 kcal/mol
Surface area39910 Å2
MethodPISA
4
F: Methanol dehydrogenase protein, large subunit
N: Methanol dehydrogenase, small subunit
H: Methanol dehydrogenase protein, large subunit
P: Methanol dehydrogenase, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5778
Polymers143,8364
Non-polymers7414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-88 kcal/mol
Surface area40070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.490, 210.290, 231.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (bacteria) / Strain: Bath / References: UniProt: Q60AR6
#2: Protein
Methanol dehydrogenase, small subunit /


Mass: 8229.256 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath / References: UniProt: Q60AR3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical
ChemComp-PQQ / PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone


Mass: 330.206 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C14H6N2O8
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2352 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaHEPES pH 7.5, 30 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.57→105.15 Å / Num. obs: 199109 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 10.5
Reflection shellResolution: 2.57→2.64 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AD7

2ad7


Resolution: 2.57→105.15 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 9930 4.99 %5
Rwork0.158 ---
obs0.16 198907 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→105.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40507 0 200 2352 43059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541907
X-RAY DIFFRACTIONf_angle_d0.93356906
X-RAY DIFFRACTIONf_dihedral_angle_d14.08115131
X-RAY DIFFRACTIONf_chiral_restr0.0355796
X-RAY DIFFRACTIONf_plane_restr0.0047403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.59920.29283290.22326221X-RAY DIFFRACTION100
2.5992-2.62980.27113160.22076254X-RAY DIFFRACTION100
2.6298-2.66190.27463340.21026232X-RAY DIFFRACTION100
2.6619-2.69560.27483150.20416228X-RAY DIFFRACTION100
2.6956-2.7310.26913370.20416267X-RAY DIFFRACTION100
2.731-2.76850.27233130.20286242X-RAY DIFFRACTION100
2.7685-2.8080.27653070.21216267X-RAY DIFFRACTION100
2.808-2.84990.28293340.21446276X-RAY DIFFRACTION100
2.8499-2.89450.24963120.18916243X-RAY DIFFRACTION100
2.8945-2.94190.26973570.19286218X-RAY DIFFRACTION100
2.9419-2.99260.2623440.1876277X-RAY DIFFRACTION100
2.9926-3.04710.25423300.18356279X-RAY DIFFRACTION100
3.0471-3.10570.22673640.17916174X-RAY DIFFRACTION100
3.1057-3.16910.23643510.16926260X-RAY DIFFRACTION100
3.1691-3.2380.21313070.16466303X-RAY DIFFRACTION100
3.238-3.31330.22073430.16676274X-RAY DIFFRACTION100
3.3133-3.39620.22433560.17656254X-RAY DIFFRACTION100
3.3962-3.4880.23193130.16036295X-RAY DIFFRACTION100
3.488-3.59070.19423440.15116256X-RAY DIFFRACTION100
3.5907-3.70660.18633460.15116275X-RAY DIFFRACTION100
3.7066-3.8390.1953100.14966323X-RAY DIFFRACTION100
3.839-3.99270.19283310.14376314X-RAY DIFFRACTION100
3.9927-4.17450.17413050.12626377X-RAY DIFFRACTION100
4.1745-4.39460.16023560.11796289X-RAY DIFFRACTION100
4.3946-4.66990.14873050.11276363X-RAY DIFFRACTION100
4.6699-5.03050.16143290.12046357X-RAY DIFFRACTION100
5.0305-5.53670.17123450.13166374X-RAY DIFFRACTION100
5.5367-6.33770.1863260.14266404X-RAY DIFFRACTION100
6.3377-7.98450.18113500.1436461X-RAY DIFFRACTION100
7.9845-105.23310.14693210.12156620X-RAY DIFFRACTION98

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