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- PDB-2ad6: crystal structure of methanol dehydrogenase from M. W3A1 (form C) -

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Basic information

Entry
Database: PDB / ID: 2ad6
Titlecrystal structure of methanol dehydrogenase from M. W3A1 (form C)
Components
  • Methanol dehydrogenase subunit 1
  • Methanol dehydrogenase subunit 2
KeywordsOXIDOREDUCTASE / methanol dehydrogenase / PQQ configuration / native
Function / homology
Function and homology information


methanol dehydrogenase (cytochrome c) / methanol oxidation / alcohol dehydrogenase (cytochrome c(L)) activity / methanol metabolic process / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / calcium ion binding / plasma 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 / Pyrrolo-quinoline quinone 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 / 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 / Methanol dehydrogenase [cytochrome c] subunit 1 / Methanol dehydrogenase [cytochrome c] subunit 2
Similarity search - Component
Biological speciesMethylophilus methylotrophus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, J. / Gan, J.-H. / Xia, Z.-X. / Mathews, F.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase
Authors: Li, J. / Gan, J.-H. / Mathews, F.S. / Xia, Z.-X.
History
DepositionJul 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 18, 2013Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methanol dehydrogenase subunit 1
B: Methanol dehydrogenase subunit 2
C: Methanol dehydrogenase subunit 1
D: Methanol dehydrogenase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2838
Polymers140,5424
Non-polymers7414
Water37,8862103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-83 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.583, 61.947, 123.804
Angle α, β, γ (deg.)90.00, 123.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2240-

HOH

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Components

#1: Protein Methanol dehydrogenase subunit 1 / MDH large alpha subunit / MEDH


Mass: 62500.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38539, EC: 1.1.99.8
#2: Protein Methanol dehydrogenase subunit 2 / MDH small beta subunit / MDH-associated peptide / MEDH


Mass: 7770.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Methylophilus methylotrophus (bacteria) / Strain: W3A1 / References: UniProt: P38540, EC: 1.1.99.8
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2103 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: macroseeding / pH: 8.25
Details: Tris-HCl, PEG 8000, methanol, pH 8.25, macroseeding, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorDetector: CCD / Date: Dec 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 204199 / Num. obs: 191743 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.132 / Num. unique all: 20338 / % possible all: 65.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.62 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 352252.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.177 18848 9.9 %RANDOM
Rwork0.156 ---
all0.158 204417 --
obs0.156 189495 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5274 Å2 / ksol: 0.353704 e/Å3
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å22.32 Å2
2---1.62 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.13 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9894 0 50 2103 12047
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.781.5
X-RAY DIFFRACTIONc_mcangle_it1.132
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.219 1268 9.9 %
Rwork0.191 11484 -
obs--62.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ccis.paramccis.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5pqq_c5tetra.parampqq_c5tetra.top

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