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- PDB-1h4i: Methylobacterium extorquens methanol dehydrogenase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1h4i
TitleMethylobacterium extorquens methanol dehydrogenase
Components
  • METHANOL DEHYDROGENASE SUBUNIT 1
  • METHANOL DEHYDROGENASE SUBUNIT 2
KeywordsDEHYDROGENASE / QUINOPROTEIN
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 / MIR / Resolution: 1.94 Å
AuthorsGhosh, M. / Anthony, C. / Harlos, K. / Goodwin, M.G. / Blake, C.
CitationJournal: Structure / Year: 1995
Title: The Refined Structure of the Quinoprotein Methanol Dehydrogenase from Methylobacterium Extorquens at 1.94 A.
Authors: Ghosh, M. / Anthony, C. / Harlos, K. / Goodwin, M.G. / Blake, C.
History
DepositionMay 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)149,4358
Polymers148,6954
Non-polymers7414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.160, 72.190, 86.170
Angle α, β, γ (deg.)86.21, 76.09, 70.44
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 65866.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) METHYLOBACTERIUM EXTORQUENS (bacteria) / References: UniProt: P16027
#2: Protein METHANOL DEHYDROGENASE SUBUNIT 2 / MDH SMALL / BETA SUBUNIT / MEDH


Mass: 8480.620 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: PYRROLO-QUINOLINE QUINONE PROSTHETIC GROUP WITH ACTIVE SITE CALCIUM IONS
Source: (natural) METHYLOBACTERIUM EXTORQUENS (bacteria) / References: UniProt: P14775, EC: 1.1.99.8
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growpH: 9 / Details: pH 9.00
Crystal grow
*PLUS
Method: other / Details: Ghosh, M., (1992) J. Mol. Biol., 228, 302.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→20 Å / Num. obs: 91350 / % possible obs: 86 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 1.94→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 4621 5 %RANDOM
Rwork0.1985 ---
obs0.1985 91350 87 %-
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10412 0 50 0 10462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.596
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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