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- PDB-1w6s: The high resolution structure of methanol dehydrogenase from meth... -

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Basic information

Entry
Database: PDB / ID: 1w6s
TitleThe high resolution structure of methanol dehydrogenase from methylobacterium extorquens
Components(METHANOL DEHYDROGENASE SUBUNIT ...) x 2
KeywordsOXIDOREDUCTASE / ANISOTROPIC / ELECTRON TRANSFER / CALCIUM-BINDING / METHANOL UTILIZATION / PQQ
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 / periplasmic space / calcium ion binding / plasma 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 / PQQ enzyme repeat / 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 2 / Methanol dehydrogenase [cytochrome c] subunit 1
Similarity search - Component
Biological speciesMETHYLOBACTERIUM EXTORQUENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWilliams, P.A. / Coates, L. / Mohammed, F. / Gill, R. / Erskine, P.T. / Wood, S.P. / Anthony, C. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The Atomic Resolution Structure of Methanol Dehydrogenase from Methylobacterium Extorquens
Authors: Williams, P.A. / Coates, L. / Mohammed, F. / Gill, R. / Erskine, P.T. / Wood, S.P. / Anthony, C. / Cooper, J.B.
History
DepositionAug 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_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_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

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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)149,65611
Polymers148,6394
Non-polymers1,0177
Water25,8881437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.900, 73.620, 88.080
Angle α, β, γ (deg.)86.09, 104.11, 109.68
Int Tables number1
Space group name H-MP1

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Components

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METHANOL DEHYDROGENASE SUBUNIT ... , 2 types, 4 molecules ACBD

#1: Protein METHANOL DEHYDROGENASE SUBUNIT 1 / MDH LARGE SUBUNIT / MEDH


Mass: 65838.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHYLOBACTERIUM EXTORQUENS (bacteria) / References: UniProt: P16027, EC: 1.1.99.8
#2: Protein METHANOL DEHYDROGENASE SUBUNIT 2 / MDH SMALL SUBUNIT / MEDH


Mass: 8480.620 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHYLOBACTERIUM EXTORQUENS (bacteria) / References: UniProt: P14775, EC: 1.1.99.8

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Non-polymers , 4 types, 1444 molecules

#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1437 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: A PRIMARY ALCOHOL + ACCEPTOR = AN ALDEHYDE + REDUCED ACCEPTOR. COFACTOR: BINDS ...CATALYTIC ACTIVITY: A PRIMARY ALCOHOL + ACCEPTOR = AN ALDEHYDE + REDUCED ACCEPTOR. COFACTOR: BINDS 1 PQQ GROUP AND 1 CALCIUM ION PER SUBUNIT. PQQ IS INSERTED BETWEEN DISULFIDE CYS130-CYS131 AND THE INDOLE RING OF TRP-270. SUBUNIT: HETEROTETRAMER COMPOSED OF 2 ALPHA AND 2 BETA SUBUNITS.
Has protein modificationY
Sequence detailsCERTAIN RESIDUES HAVE NO DENSITY THEREFORE THESE HAVE BEEN MODELLED AS ALANINES. THE MISSING ATOMS ...CERTAIN RESIDUES HAVE NO DENSITY THEREFORE THESE HAVE BEEN MODELLED AS ALANINES. THE MISSING ATOMS FOR THESE RESIDUES ARE LISTED IN REMARK 470.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 38 %

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.23→20 Å / Num. obs: 373341 / % possible obs: 90.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 2.3

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Processing

SoftwareName: SHELXL-97 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→10 Å / Num. parameters: 106187 / Num. restraintsaints: 129254 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 18605 5.3 %RANDOM
all0.1527 353944 --
obs0.1576 -85 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 11797.25
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10340 0 68 1437 11845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.022
X-RAY DIFFRACTIONs_angle_d0.046
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0318
X-RAY DIFFRACTIONs_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.127
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.068

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