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- PDB-6oc5: Lanthanide-dependent methanol dehydrogenase XoxF from Methylobact... -

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Basic information

Entry
Database: PDB / ID: 6oc5
TitleLanthanide-dependent methanol dehydrogenase XoxF from Methylobacterium extorquens, in complex with Lanthanum
ComponentsLanthanide-dependent methanol dehydrogenase XoxF
KeywordsOXIDOREDUCTASE / XoxF / La / methanol
Function / homology
Function and homology information


lanthanide-dependent methanol dehydrogenase / methanol metabolic process / 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 / 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 ...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 / Mainly Beta
Similarity search - Domain/homology
LANTHANUM (III) ION / Lanthanide-dependent methanol dehydrogenase
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)130,2264
Polymers129,9482
Non-polymers2782
Water1267
1
A: Lanthanide-dependent methanol dehydrogenase XoxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1132
Polymers64,9741
Non-polymers1391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lanthanide-dependent methanol dehydrogenase XoxF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1132
Polymers64,9741
Non-polymers1391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.320, 87.952, 202.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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


Mass: 138.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: La / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.99 Å3/Da / Density % sol: 38.34 % / Mosaicity: 0.47 °
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% Propanol, 0.1M HEPES pH 7.5, 20% PEG 4000

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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: 2.8→48.61 Å / Num. obs: 25837 / % possible obs: 97.7 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.051 / Rrim(I) all: 0.109 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.953.40.5121148033400.7890.3120.602288.2
8.85-48.613.90.04735739250.9950.0250.05417.997.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18rc1-3769refinement
XDSdata reduction
Aimless0.5.23data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAE

4mae


Resolution: 2.8→48.61 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 31.02
RfactorNum. reflection% reflection
Rfree0.2802 2351 4.98 %
Rwork0.2493 --
obs0.2509 25783 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.23 Å2 / Biso mean: 65.1889 Å2 / Biso min: 35.58 Å2
Refinement stepCycle: final / Resolution: 2.8→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8424 0 2 7 8433
Biso mean--67.57 55.66 -
Num. residues----1158
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3488X-RAY DIFFRACTION2.444TORSIONAL
12B3488X-RAY DIFFRACTION2.444TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.860.4204640.34971900196467
2.86-2.920.35661520.35152645279795
2.92-2.990.37051130.34712628274196
2.99-3.060.36921370.33662694283196
3.06-3.140.32231730.32842636280997
3.14-3.240.34571450.29492679282496
3.24-3.340.30181480.28992654280297
3.34-3.460.3021340.26832668280297
3.46-3.60.30651310.25352710284197
3.6-3.760.28441460.26622713285998
3.76-3.960.28221450.25282694283998
3.96-4.210.31611520.23682711286398
4.21-4.530.22921320.20912672280498
4.53-4.990.26641270.20472737286498
4.99-5.710.25811560.232696285298
5.71-7.190.22681340.23192712284698
7.19-48.610.24891620.21832695285798
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)
12.1725-1.31210.34323.7222-0.81570.9916-0.4435-0.1778-0.23750.69430.36881.3305-0.3105-0.1518-0.04870.4110.03520.28150.55340.22340.7577-26.711836.4873-22.3382
22.5653-1.3411-0.24923.1895-0.761.41590.22350.4666-0.0415-0.4884-0.20320.923-0.5014-0.21750.02290.43280.0135-0.14050.60690.16820.7421-28.683449.8844-42.809
32.5877-0.8840.50583.4858-0.48271.91140.21680.58420.4774-0.448-0.30630.3881-0.1231-0.03860.12150.3378-0.08010.05260.69030.12760.3835-16.35941.2272-42.7626
44.66120.5436-0.10516.90350.17252.9585-0.14860.215-0.2124-0.12790.1590.5091-0.38710.1784-0.02060.1597-0.0471-0.02430.40890.12240.3191-9.687634.4689-30.0687
53.653-1.59330.60886.1728-0.90913.43970.13870.2487-0.4511-0.3909-0.11080.30120.29760.1460.00950.2072-0.0773-0.04920.44310.04040.2641-1.47678.207-29.0301
62.18520.8655-1.68066.5278-0.73054.63410.1919-0.1278-0.56270.18190.07070.41160.2937-0.3257-0.27870.32380.0071-0.15280.45770.12410.5146-0.6157-12.208-16.135
74.681-0.0919-0.78335.75322.23357.05870.109-0.0673-0.77591.0143-0.08651.02790.5773-0.13450.01230.6049-0.01370.11310.6580.26880.7495-9.5162-9.77340.9086
88.94861.5529-2.88173.8703-0.80661.42560.4313-0.3646-0.94580.993-0.1540.4972-0.0988-0.2133-0.27870.89510.01680.06360.52350.20550.6396-9.03562.1695-7.1323
92.66-2.46851.18694.4198-1.03344.12960.134-0.5585-0.37311.17660.23630.2702-0.3487-0.2998-0.17370.4362-0.001-0.03460.52240.15960.2937-3.72215.5902-12.7819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 214 )A22 - 214
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 442 )A215 - 442
3X-RAY DIFFRACTION3chain 'A' and (resid 443 through 503 )A443 - 503
4X-RAY DIFFRACTION4chain 'A' and (resid 504 through 600 )A504 - 600
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 193 )B22 - 193
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 364 )B194 - 364
7X-RAY DIFFRACTION7chain 'B' and (resid 365 through 412 )B365 - 412
8X-RAY DIFFRACTION8chain 'B' and (resid 413 through 476 )B413 - 476
9X-RAY DIFFRACTION9chain 'B' and (resid 477 through 600 )B477 - 600

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