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- PDB-6fkw: Europium-containing methanol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6fkw
TitleEuropium-containing methanol dehydrogenase
ComponentsMethanol dehydrogenase
KeywordsOXIDOREDUCTASE / Rare earth element / methanol dehydrogenase / PQQ
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c) activity / alcohol dehydrogenase (cytochrome c) / alcohol dehydrogenase (cytochrome c(L)) activity / methanol dehydrogenase (cytochrome c) / calcium ion binding / membrane
Similarity search - Function
PQQ-like domain / Quinoprotein alcohol dehydrogenase-like superfamily / 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 / Mainly Beta
Similarity search - Domain/homology
EUROPIUM ION / PYRROLOQUINOLINE QUINONE / Methanol dehydrogenase
Similarity search - Component
Biological speciesMethylacidiphilum fumariolicum SolV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsBarends, T. / Dietl, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
ERCERC Advanced Grant project VOLCANO 669371 Netherlands
CitationJournal: Chembiochem / Year: 2018
Title: Similar but not the same: First Kinetic and Structural Analyses of a Methanol Dehydrogenase Containing a Europium Ion in the Active Site.
Authors: Jahn, B. / Pol, A. / Lumpe, H. / Barends, T. / Dietl, A. / Hogendoorn, C. / Op den Camp, H. / Daumann, L.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methanol dehydrogenase
B: Methanol dehydrogenase
C: Methanol dehydrogenase
D: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,53112
Polymers254,6024
Non-polymers1,9298
Water27,5271528
1
A: Methanol dehydrogenase
C: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2656
Polymers127,3012
Non-polymers9644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-46 kcal/mol
Surface area34310 Å2
MethodPISA
2
B: Methanol dehydrogenase
D: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2656
Polymers127,3012
Non-polymers9644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-46 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.080, 101.180, 107.790
Angle α, β, γ (deg.)115.21, 97.53, 91.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Methanol dehydrogenase


Mass: 63650.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Methylacidiphilum fumariolicum SolV (bacteria)
References: UniProt: I0JWN7, methanol dehydrogenase (cytochrome c), alcohol dehydrogenase (cytochrome c)
#2: Chemical
ChemComp-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Eu
#3: Chemical
ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1528 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 24% w/v PEG 8000, 0.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9773 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9773 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 352259 / % possible obs: 90.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 11.5
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4MAE

4mae


Resolution: 1.4→96.27 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.997 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18484 18419 5 %RANDOM
Rwork0.16855 ---
obs0.16939 352259 90.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.059 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å2-0.01 Å20.02 Å2
2---0.24 Å20.14 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 1.4→96.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17940 0 100 1528 19568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0218609
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217013
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.9425352
X-RAY DIFFRACTIONr_angle_other_deg0.731339168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62252310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58424.463838
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.826152846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0481572
X-RAY DIFFRACTIONr_chiral_restr0.0650.22602
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02121484
X-RAY DIFFRACTIONr_gen_planes_other00.024420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.3139225
X-RAY DIFFRACTIONr_mcbond_other0.6441.3139224
X-RAY DIFFRACTIONr_mcangle_it1.0221.9711528
X-RAY DIFFRACTIONr_mcangle_other1.0221.9711529
X-RAY DIFFRACTIONr_scbond_it1.0671.4459384
X-RAY DIFFRACTIONr_scbond_other1.0671.4459381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6772.11413818
X-RAY DIFFRACTIONr_long_range_B_refined5.95912.29922892
X-RAY DIFFRACTIONr_long_range_B_other5.84411.65922300
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 1334 -
Rwork0.369 24802 -
obs--86.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6062-0.13330.02122.0664-0.26880.5422-0.0489-0.1194-0.11070.24690.13330.28730.0727-0.0384-0.08440.31130.05570.03780.1754-0.02580.1411-28.542-75.8287-55.6344
20.6279-0.19810.10050.6724-0.11870.4053-0.01650.00660.0588-0.02910.0150.0279-0.0052-0.01540.00140.01-0.02340.0020.1004-0.05560.0629-17.6907-14.2695-11.3558
30.3136-0.04990.0611.01830.02250.7272-0.04040.01770.01-0.04010.0352-0.0247-0.0160.05570.00520.0454-0.00770.0180.1302-0.0460.0603-19.8604-29.2809-63.5377
40.40670.1402-0.03591.3032-0.17550.36950.01710.0054-0.0359-0.0522-0.0251-0.04540.075-0.02560.0080.0409-0.0320.00120.1128-0.04880.0506-3.1294-59.989-9.4839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 576
2X-RAY DIFFRACTION1D602
3X-RAY DIFFRACTION1D601
4X-RAY DIFFRACTION2A1 - 576
5X-RAY DIFFRACTION2A602
6X-RAY DIFFRACTION2A601
7X-RAY DIFFRACTION3B1 - 576
8X-RAY DIFFRACTION3B602
9X-RAY DIFFRACTION3B601
10X-RAY DIFFRACTION4C1 - 576
11X-RAY DIFFRACTION4C602
12X-RAY DIFFRACTION4C601

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