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- PDB-1g72: CATALYTIC MECHANISM OF QUINOPROTEIN METHANOL DEHYDROGENASE: A THE... -

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Basic information

Entry
Database: PDB / ID: 1g72
TitleCATALYTIC MECHANISM OF QUINOPROTEIN METHANOL DEHYDROGENASE: A THEORETICAL AND X-RAY CRYSTALLOGRAPHIC INVESTIGATION
Components
  • METHANOL DEHYDROGENASE HEAVY SUBUNIT
  • METHANOL DEHYDROGENASE LIGHT SUBUNIT
KeywordsOXIDOREDUCTASE / Quinoprotein
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c(L)) activity / methanol dehydrogenase (cytochrome c) / methanol oxidation / 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: 1.9 Å
AuthorsZheng, Y. / Xia, Z. / Chen, Z. / Bruice, T.C. / Mathews, F.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation.
Authors: Zheng, Y.J. / Xia, Z.x. / Chen, Z.w. / Mathews, F.S. / Bruice, T.C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: DETERMINATION OF THE GENE SEQUENCE AND THE THREE-DIMENSIONAL STRUCTURE AT 2.4 ANGSTROMS RESOLUTION OF METHANOL DEHYDROGENASE FROM METHYLOPHILUS W3A1
Authors: Xia, Z. / Dai, W. / ZHANG, Y. / WHITE, S.A. / BOYD, G.D. / Mathews, F.S.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionJan 24, 2001ID: 1B2N
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 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 / 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_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 / _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 HEAVY SUBUNIT
B: METHANOL DEHYDROGENASE LIGHT SUBUNIT
C: METHANOL DEHYDROGENASE HEAVY SUBUNIT
D: METHANOL DEHYDROGENASE LIGHT SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,6888
Polymers140,9474
Non-polymers7414
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-74 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.115, 69.744, 109.838
Angle α, β, γ (deg.)90.00, 110.29, 90.00
Int Tables number4
Space group name H-MP1211
DetailsMETHANOL DEHYDROGENASE IS AN A2B2 TETRAMER. THE ASYMMETRIC UNIT CONTAINS THE TETRAMER, TWO PYRROLOQUINOLINE QUINONE COFACTORS (PQQ) AND 2 CALCIUM IONS. A NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS RELATES THE TWO HALVES.

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Components

#1: Protein METHANOL DEHYDROGENASE HEAVY SUBUNIT / MDH LARGE ALPHA SUBUNIT


Mass: 62702.828 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 LIGHT SUBUNIT / MDH SMALL ALPHA SUBUNIT


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.: 614 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 295 K / Method: directly mixing / pH: 8.2
Details: PEG 8000, tris-HCl, Methanol, pH 8.2, Directly mixing, temperature 295.0K
Crystal grow
*PLUS
pH: 9.2 / Method: vapor diffusion / Details: Oubrie, A., (1999) J.Mol.Biol., 289, 319.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
20.1 mMPQQ1drop
38 %(w/v)PEG60001drop
450 mMTris-glycine1drop
520-23 %(w/v)PEG60001reservoir
6120 mM1reservoirNaCl
73 mM1reservoirCaCl2
850 mMTris-glycine1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 109884 / Num. obs: 108348 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.9 / Num. unique all: 10453 / % possible all: 95.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AAH

4aah


Resolution: 1.9→100 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1898 10173 -RANDOM
Rwork0.1605 ---
obs0.1605 101579 92.5 %-
all-109847 --
Displacement parametersBiso mean: 25.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9710 0 50 614 10374
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.304 842 -
Rwork0.281 --
obs-8621 75 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.281

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