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- PDB-6oc6: Lanthanide-dependent methanol dehydrogenase XoxF from Methylobact... -

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Basic information

Entry
Database: PDB / ID: 6oc6
TitleLanthanide-dependent methanol dehydrogenase XoxF from Methylobacterium extorquens, in complex with Lanthanum and Pyrroloquinoline quinone
ComponentsLanthanide-dependent methanol dehydrogenase XoxF
KeywordsOXIDOREDUCTASE / XoxF / La / methanol / Pyrroloquinoline quinone / PQQ
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 / Methanol dehydrogenase
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.89 Å
AuthorsFellner, M. / Good, N.M. / Martinez-Gomez, N.C. / Hausinger, R.P. / Hu, J.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function.
Authors: Good, N.M. / Fellner, M. / Demirer, K. / Hu, J. / Hausinger, R.P. / Martinez-Gomez, N.C.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)130,8866
Polymers129,9482
Non-polymers9384
Water46826
1
A: Lanthanide-dependent methanol dehydrogenase XoxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4433
Polymers64,9741
Non-polymers4692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanthanide-dependent methanol dehydrogenase XoxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4433
Polymers64,9741
Non-polymers4692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.272, 101.941, 103.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 22 through 26 or (resid 27...
21(chain B and ((resid 22 through 24 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEU(chain A and (resid 22 through 26 or (resid 27...AA22 - 2622 - 26
12LYSLYSLYSLYS(chain A and (resid 22 through 26 or (resid 27...AA2727
13ASNASNASNASN(chain A and (resid 22 through 26 or (resid 27...AA22 - 60022 - 600
14ASNASNASNASN(chain A and (resid 22 through 26 or (resid 27...AA22 - 60022 - 600
15ASNASNASNASN(chain A and (resid 22 through 26 or (resid 27...AA22 - 60022 - 600
16ASNASNASNASN(chain A and (resid 22 through 26 or (resid 27...AA22 - 60022 - 600
21ASNASNSERSER(chain B and ((resid 22 through 24 and (name N...BB22 - 2422 - 24
22ASNASNASNASN(chain B and ((resid 22 through 24 and (name N...BB22 - 60022 - 600
23ASNASNASNASN(chain B and ((resid 22 through 24 and (name N...BB22 - 60022 - 600
24ASNASNASNASN(chain B and ((resid 22 through 24 and (name N...BB22 - 60022 - 600
25ASNASNASNASN(chain B and ((resid 22 through 24 and (name N...BB22 - 60022 - 600

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Components

#1: Protein Lanthanide-dependent methanol dehydrogenase XoxF


Mass: 64974.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: xoxF, MexAM1_META1p1740 / Production host: Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5B120
#2: Chemical ChemComp-LA / LANTHANUM (III) ION / Lanthanum


Mass: 138.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE / Pyrroloquinoline quinone


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 39.91 % / Mosaicity: 0.23 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M Ammonium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.89→40 Å / Num. obs: 24645 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.15 / Rrim(I) all: 0.339 / Χ2: 1.023 / Net I/σ(I): 2.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-34.71.0223880.5250.5091.1450.90898.7
3-3.124.90.82324290.6440.4070.9210.92799.8
3.12-3.274.90.67724170.7120.3350.7580.994100
3.27-3.444.90.50424280.8480.2480.5631.083100
3.44-3.654.90.37124410.9070.1830.4151.096100
3.65-3.944.90.29824590.9320.1470.3331.057100
3.94-4.334.90.22824490.9640.1110.2551.063100
4.33-4.964.90.16924840.9810.0830.1881.025100
4.96-6.244.80.19325020.9720.0960.2171.089100
6.24-404.60.1126480.990.0560.1240.97100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.32 Å34.06 Å
Translation4.32 Å34.06 Å

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Processing

Software
NameVersionClassification
PHENIX1.18rc1-3769refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OC5

6oc5


Resolution: 2.89→36.35 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.64
RfactorNum. reflection% reflection
Rfree0.2581 1115 4.53 %
Rwork0.2037 --
obs0.2062 24609 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.54 Å2 / Biso mean: 26.113 Å2 / Biso min: 3.31 Å2
Refinement stepCycle: final / Resolution: 2.89→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8614 0 50 26 8690
Biso mean--29.52 20.44 -
Num. residues----1158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3494X-RAY DIFFRACTION3.622TORSIONAL
12B3494X-RAY DIFFRACTION3.622TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.020.38251410.29042797293897
3.02-3.180.35631230.26729163039100
3.18-3.380.30651480.23428993047100
3.38-3.640.25421180.203329363054100
3.64-40.22751240.199329383062100
4.01-4.580.21671790.165228983077100
4.58-5.770.22781290.174230063135100
5.77-36.350.23561530.185331043257100

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