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- PDB-4mae: Methanol dehydrogenase from Methylacidiphilum fumariolicum SolV -

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Basic information

Entry
Database: PDB / ID: 4mae
TitleMethanol dehydrogenase from Methylacidiphilum fumariolicum SolV
ComponentsMethanol dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / PQQ / lanthanide ion / cerium ion
Function / homology
Function and homology information


lanthanide-dependent methanol dehydrogenase / alcohol dehydrogenase (cytochrome c) activity / alcohol dehydrogenase (cytochrome c(L)) activity / 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
CERIUM (III) ION / PYRROLOQUINOLINE QUINONE / Lanthanide-dependent methanol dehydrogenase
Similarity search - Component
Biological speciesMethylacidiphilum fumariolicum SolV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPol, A.J. / Barends, T.R.M. / Dietl, A. / Khadem, A.F. / Eygenstein, J. / Jetten, M.S.M. / Op den Camp, H.J.M.
CitationJournal: ENVIRON.MICROBIOL. / Year: 2014
Title: Rare earth metals are essential for methanotrophic life in volcanic mudpots.
Authors: Pol, A. / Barends, T.R. / Dietl, A. / Khadem, A.F. / Eygensteyn, J. / Jetten, M.S. / Op den Camp, H.J.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Oct 25, 2017Group: Advisory / Author supporting evidence
Category: pdbx_struct_assembly_auth_evidence / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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_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 / _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
B: Methanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3018
Polymers127,3012
Non-polymers4,0006
Water19,5461085
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-44 kcal/mol
Surface area34610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 75.500, 136.400
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE DIMERIZATION IS CONFIRMED BY ANALYTICAL ULTRACENTRIFUGATION.

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Components

#1: Protein Methanol dehydrogenase


Mass: 63650.480 Da / Num. of mol.: 2 / Fragment: UNP residues 35-611 / 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-CE / CERIUM (III) ION


Mass: 140.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ce
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: RESERVOIR: 22%w/v PEG 8000, 0.2M NaCl, without buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9718 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 125838 / % possible obs: 89.7 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -999 / Redundancy: 2.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.9 / % possible all: 55.8

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Processing

Software
NameVersionClassification
HEIDIdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.645 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): -999 / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18895 6623 5 %RANDOM
Rwork0.16125 ---
obs0.16263 125838 89.689 %-
all-125838 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.49 Å2
2---0.27 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8988 0 57 1085 10130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229339
X-RAY DIFFRACTIONr_bond_other_d0.0010.026213
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.94312727
X-RAY DIFFRACTIONr_angle_other_deg0.84315118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90751160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31724.515423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.549151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9851536
X-RAY DIFFRACTIONr_chiral_restr0.070.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021925
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_it0.4021.55705
X-RAY DIFFRACTIONr_mcbond_other0.0941.52389
X-RAY DIFFRACTIONr_mcangle_it0.75629145
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.30933634
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1384.53579
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 251 -
Rwork0.267 4772 -
obs--100 %

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