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- PDB-5xm3: Crystal Structure of Methanol dehydrogenase from Methylophaga ami... -

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Basic information

Entry
Database: PDB / ID: 5xm3
TitleCrystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans
Components
  • Glucose dehydrogenase
  • Methanol dehydrogenase [cytochrome c] subunit 2
KeywordsOXIDOREDUCTASE / marine / methanol dehydrogenase / methylophaga / pyrroloquinoline quinone / Mg++
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 / Pyrrolo-quinoline quinone repeat / PQQ-like domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Few Secondary Structures / Irregular / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Glucose dehydrogenase / Methanol dehydrogenase [cytochrome c] subunit 2
Similarity search - Component
Biological speciesMethylophaga aminisulfidivorans MP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsCao, T.P. / Choi, J.M. / Lee, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Chosun University2015 Korea, Republic Of
CitationJournal: J. Microbiol. / Year: 2018
Title: The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT
Authors: Cao, T.P. / Choi, J.M. / Kim, S.W. / Lee, S.H.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / struct_keywords
Item: _citation.journal_issue / _citation.journal_volume ..._citation.journal_issue / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _struct.pdbx_descriptor / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose dehydrogenase
B: Methanol dehydrogenase [cytochrome c] subunit 2
C: Glucose dehydrogenase
D: Methanol dehydrogenase [cytochrome c] subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,3508
Polymers158,6414
Non-polymers7094
Water17,601977
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-53 kcal/mol
Surface area40650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.926, 109.479, 95.554
Angle α, β, γ (deg.)90.00, 100.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glucose dehydrogenase / Methanol dehydrogenase large subunit


Mass: 69341.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Gene: MAMP_01209
Production host: Methylophaga aminisulfidivorans MP (bacteria)
References: UniProt: A3FJ48
#2: Protein Methanol dehydrogenase [cytochrome c] subunit 2 / MDH small subunit beta / MDH-associated peptide / MEDH


Mass: 9978.702 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Gene: MAMP_01202
Production host: Methylophaga aminisulfidivorans MP (bacteria)
References: UniProt: A3FJ51, methanol dehydrogenase (cytochrome c)
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH 6.5, 0.2M magnesium acetate tetrahydrate, 10%(v/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2009
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 140904 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 24.55
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.827 / Num. unique obs: 6897 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W6S

1w6s


Resolution: 1.701→34.724 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 7071 5.02 %
Rwork0.1511 --
obs0.1526 140904 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→34.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10376 0 50 977 11403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310763
X-RAY DIFFRACTIONf_angle_d1.11214579
X-RAY DIFFRACTIONf_dihedral_angle_d13.2363860
X-RAY DIFFRACTIONf_chiral_restr0.0441454
X-RAY DIFFRACTIONf_plane_restr0.0061900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7007-1.72010.24792310.20064250X-RAY DIFFRACTION95
1.7201-1.74030.23282390.19774408X-RAY DIFFRACTION99
1.7403-1.76150.24112240.18424451X-RAY DIFFRACTION100
1.7615-1.78380.20892230.17324462X-RAY DIFFRACTION99
1.7838-1.80730.20942350.16894410X-RAY DIFFRACTION99
1.8073-1.83210.1992300.16724447X-RAY DIFFRACTION99
1.8321-1.85820.23432390.16754449X-RAY DIFFRACTION100
1.8582-1.8860.22222200.16144458X-RAY DIFFRACTION99
1.886-1.91540.18632310.1614457X-RAY DIFFRACTION100
1.9154-1.94680.19362470.15444437X-RAY DIFFRACTION99
1.9468-1.98040.18932340.15254468X-RAY DIFFRACTION100
1.9804-2.01640.18212340.15294454X-RAY DIFFRACTION100
2.0164-2.05520.18852360.15334437X-RAY DIFFRACTION100
2.0552-2.09710.19242310.15524477X-RAY DIFFRACTION100
2.0971-2.14270.1922170.15374487X-RAY DIFFRACTION100
2.1427-2.19260.18672330.1524483X-RAY DIFFRACTION100
2.1926-2.24740.18682340.14774440X-RAY DIFFRACTION100
2.2474-2.30810.19352670.14934465X-RAY DIFFRACTION100
2.3081-2.3760.18132350.15544482X-RAY DIFFRACTION100
2.376-2.45270.19392170.15534479X-RAY DIFFRACTION100
2.4527-2.54040.19352510.15914476X-RAY DIFFRACTION100
2.5404-2.6420.20332580.16314454X-RAY DIFFRACTION100
2.642-2.76220.1982250.1584499X-RAY DIFFRACTION100
2.7622-2.90780.19442000.16244531X-RAY DIFFRACTION100
2.9078-3.08990.2012180.174489X-RAY DIFFRACTION100
3.0899-3.32830.18712720.15864445X-RAY DIFFRACTION100
3.3283-3.66290.17352490.14744489X-RAY DIFFRACTION100
3.6629-4.19210.14222560.13084472X-RAY DIFFRACTION100
4.1921-5.27860.12392350.11254520X-RAY DIFFRACTION99
5.2786-34.73150.15472500.13184557X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.8433 Å / Origin y: -1.0738 Å / Origin z: 27.8722 Å
111213212223313233
T0.1116 Å2-0.0211 Å2-0.0163 Å2-0.0924 Å2-0.009 Å2--0.1084 Å2
L0.3224 °2-0.1575 °2-0.218 °2-0.2264 °20.1615 °2--0.3357 °2
S0.0252 Å °-0.0351 Å °-0.0007 Å °-0.0259 Å °-0.0274 Å °0.0135 Å °-0.0115 Å °-0.0069 Å °0.0016 Å °
Refinement TLS groupSelection details: all

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