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- PDB-6dam: Crystal structure of lanthanide-dependent methanol dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 6dam
TitleCrystal structure of lanthanide-dependent methanol dehydrogenase XoxF from Methylomicrobium buryatense 5G
ComponentsLanthanide-dependent methanol dehydrogenase XoxF
KeywordsOXIDOREDUCTASE / dehydrogenase / PQQ / methanol / XoxF / lanthanide / lanthanum / methanotroph
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / outer membrane-bounded periplasmic space / calcium ion binding / membrane
Similarity search - Function
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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 8 Propeller ...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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 8 Propeller / Methanol Dehydrogenase; Chain A / Quinoprotein alcohol dehydrogenase-like superfamily / Mainly Beta
Similarity search - Domain/homology
LANTHANUM (III) ION / PYRROLOQUINOLINE QUINONE / Lanthanide-dependent methanol dehydrogenase XoxF
Similarity search - Component
Biological speciesMethylomicrobium buryatense 5G (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDeng, Y. / Ro, S.Y. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM118035 United States
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Structure and function of the lanthanide-dependent methanol dehydrogenase XoxF from the methanotroph Methylomicrobium buryatense 5GB1C.
Authors: Deng, Y.W. / Ro, S.Y. / Rosenzweig, A.C.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lanthanide-dependent methanol dehydrogenase XoxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7714
Polymers67,2791
Non-polymers4923
Water8,953497
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.347, 92.283, 191.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1231-

HOH

21A-1272-

HOH

31A-1295-

HOH

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Components

#1: Protein Lanthanide-dependent methanol dehydrogenase XoxF


Mass: 67278.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methylomicrobium buryatense 5G (bacteria) / Plasmid details: Lidstrom Lab / References: UniProt: A0A3F2YLY8*PLUS
#2: Chemical ChemComp-LA / LANTHANUM (III) ION


Mass: 138.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: La
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 1.82 Å3/Da / Density % sol: 32.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, and 20% PEG 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.979
SYNCHROTRONAPS 23-ID-B21.968
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJun 6, 2017
DECTRIS EIGER X 16M2PIXELJun 7, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.9681
ReflectionResolution: 1.85→30 Å / Num. obs: 39629 / % possible obs: 93.6 % / Redundancy: 9.7 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.14 / Net I/σ(I): 51
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 9.2 / CC1/2: 0.854 / Rpim(I) all: 0.267 / Rrim(I) all: 0.865 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAE

4mae


Resolution: 1.85→27.674 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 2013 5.08 %
Rwork0.1515 37608 -
obs0.1531 39621 93.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.32 Å2 / Biso mean: 22.2327 Å2 / Biso min: 10.58 Å2
Refinement stepCycle: final / Resolution: 1.85→27.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 26 497 4901
Biso mean--19.57 31.75 -
Num. residues----563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074526
X-RAY DIFFRACTIONf_angle_d0.8916175
X-RAY DIFFRACTIONf_chiral_restr0.058649
X-RAY DIFFRACTIONf_plane_restr0.005795
X-RAY DIFFRACTIONf_dihedral_angle_d4.572578
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.89630.2695950.22972308240381
1.8963-1.94760.25171360.19872345248183
1.9476-2.00490.19161320.18262443257586
2.0049-2.06960.23731230.17572533265689
2.0696-2.14350.19971480.17392609275792
2.1435-2.22930.22231450.17012641278693
2.2293-2.33070.21081160.15762689280594
2.3307-2.45350.21371530.15932693284695
2.4535-2.60710.1871740.16152749292397
2.6071-2.80830.20521550.16162860301599
2.8083-3.09050.16471560.15628733029100
3.0905-3.5370.1751510.142628953046100
3.537-4.45320.1361670.12129233090100
4.4532-27.67660.16061620.131430473209100
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)
10.49060.0131-0.11770.53560.10130.68530.03090.02570.0567-0.0412-0.01120.0634-0.0195-0.1238-0.00320.14120.0215-0.00810.1745-0.01430.1461-8.4542112.948421.8475
20.8390.2414-0.23770.87880.28561.20930.0363-0.0569-0.0306-0.032-0.00360.02470.106-0.1623-0.01960.1459-0-0.02440.14760.00220.1253-0.5022104.366337.3703
30.55910.35290.07050.63940.00491.13520.0278-0.0028-0.01030.0107-0.0214-0.0412-0.00790.1208-0.00530.11970.0216-0.01340.13950.00090.133612.8748114.116835.6807
40.65040.24830.0070.59230.01671.00820.03590.08510.0571-0.071-0.0208-0.0053-0.0807-0.0012-0.00990.14840.03830.0110.16020.00550.14154.0784121.802312.2654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 413 through 515 )A413 - 515
2X-RAY DIFFRACTION2chain 'A' and (resid 516 through 617 )A516 - 617
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 168 )A27 - 168
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 412 )A169 - 412

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