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- PDB-1lrw: Crystal structure of methanol dehydrogenase from P. denitrificans -

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Basic information

Entry
Database: PDB / ID: 1lrw
TitleCrystal structure of methanol dehydrogenase from P. denitrificans
Components
  • methanol dehydrogenase subunit 1
  • methanol dehydrogenase subunit 2
KeywordsOXIDOREDUCTASE / Heavy subunits: 8-fold beta-propeller superbarrel
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 / membrane
Similarity search - Function
Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Bacterial quinoprotein dehydrogenases signature 1. / 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 ...Methanol Dehydrogenase; Chain B / Methanol dehydrogenase, beta subunit / Bacterial quinoprotein dehydrogenases signature 1. / 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 / Glucose/ethanol/alcohol dehydrogenase, beta-propeller domain / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / 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 speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXia, Z.-X. / Dai, W.-W. / He, Y.-N. / White, S.A. / Mathews, F.S. / Davidson, V.L.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i
Authors: Xia, Z.-X. / Dai, W.-W. / He, Y.-N. / White, S.A. / Mathews, F.S. / Davidson, V.L.
History
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / 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_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
Remark 999 sequence authors state that the published sequence of ALA 444- ALA 449, ALA 451 and VAL 490 does ... sequence authors state that the published sequence of ALA 444- ALA 449, ALA 451 and VAL 490 does not match the electron density. Based on the electron density, they established the x-ray sequence Gly 444- Ser 450, Leu 452 and ALA 490 in which Gly 447 is an insertion.

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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)153,2958
Polymers152,5554
Non-polymers7414
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-101 kcal/mol
Surface area42700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.340, 122.280, 107.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein methanol dehydrogenase subunit 1 / mdh large alpha subunit / medh


Mass: 66811.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P12293, EC: 1.1.99.8
#2: Protein methanol dehydrogenase subunit 2 / mdh small beta subunit / medh


Mass: 9465.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: P29898, 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.: 403 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: seeding / pH: 8.3
Details: PEG 3350, Tris-HCl, Li2SO4, pH 8.3, seeding, temperature 293K
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlenzyme1drop
20.1 MTris-HCl1reservoirpH8.5
330 %PEG40001reservoir
40.2 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.49 Å / Num. all: 52799 / Num. obs: 49524 / % possible obs: 93.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.093 / Net I/σ(I): 13.9
Reflection shellResolution: 2.49→2.68 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 7330 / Rsym value: 0.262 / % possible all: 70.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 317794 / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 70.1 % / Rmerge(I) obs: 0.262

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Processing

Software
NameVersionClassification
MERLOTphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4AAH

4aah


Resolution: 2.5→19.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 53755.76 / Data cutoff high rms absF: 53755.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: non-crystallographic symmetry restraint was not applied
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4953 10.1 %RANDOM
Rwork0.179 ---
obs0.179 49218 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9669 Å2 / ksol: 0.311306 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-10.72 Å20 Å20 Å2
2---2.18 Å20 Å2
3----8.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10734 0 50 403 11187
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.394 267 9.7 %
Rwork0.353 2494 -
obs--53.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PQQ.PARPQQ.TOP
X-RAY DIFFRACTION4CCIS.parCCIS.top
X-RAY DIFFRACTION5ION.PARAMION.Top
Refinement
*PLUS
Highest resolution: 2.49 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.73
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2.49 Å / Lowest resolution: 2.68 Å

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