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- PDB-6zcv: Crystal structure of lanthanide-dependent alcohol dehydrogenase P... -

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Basic information

Entry
Database: PDB / ID: 6zcv
TitleCrystal structure of lanthanide-dependent alcohol dehydrogenase PedH from Pseudomonas putida KT2440
ComponentsQuinoprotein ethanol dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c) activity / alcohol dehydrogenase (cytochrome c) / outer membrane-bounded periplasmic space / calcium ion binding / membrane
Similarity search - Function
PQQ-dependent type I alcohol dehydrogenase / 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 / 8 Propeller / Methanol Dehydrogenase; Chain A ...PQQ-dependent type I alcohol dehydrogenase / 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 / 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
PYRROLOQUINOLINE QUINONE / PRASEODYMIUM ION / Quinoprotein ethanol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBange, G. / Lepak, A. / Elsayed, E.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Acs Catalysis / Year: 2020
Title: Engineered PQQ-Dependent Alcohol Dehydrogenase for the Oxidation of 5-(Hydroxymethyl)furoic Acid
Authors: Wehrmann, M. / Elsayed, E.M. / Koebbing, S. / Bendz, L. / Lepak, A. / Schwabe, J. / Wierckx, N. / Bange, G. / Klebensberger, J.
History
DepositionJun 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Quinoprotein ethanol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2225
Polymers65,6191
Non-polymers6034
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-32 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.530, 105.530, 186.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1177-

HOH

21A-1384-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Quinoprotein ethanol dehydrogenase


Mass: 65619.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: qedH-II, PP_2679 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q88JH0, alcohol dehydrogenase (cytochrome c)

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Non-polymers , 5 types, 589 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H6N2O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pr / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.25 mM PedHF412V/W561A was co-crystallized with equimolar concentration of PQQ and metal of PrCl3 within 24h days in 0.2 M Lithium sulfate, 0.1 M sodium cacodylate pH = 6.5, 30 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.6→47.72 Å / Num. obs: 115355 / % possible obs: 99.97 % / Redundancy: 27 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.1783 / Net I/σ(I): 15.92
Reflection shellResolution: 1.704→1.765 Å / Num. unique obs: 11332 / CC1/2: 0.677

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1flg

1flg


Resolution: 1.7→47.19 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1601 5766 5 %
Rwork0.1417 109577 -
obs0.1426 115343 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.83 Å2 / Biso mean: 26.3014 Å2 / Biso min: 12.6 Å2
Refinement stepCycle: final / Resolution: 1.7→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 43 585 4969
Biso mean--28.66 35.17 -
Num. residues----562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.720.2741880.240335753763
1.72-1.740.26691900.225336093799
1.74-1.760.23561890.216935813770
1.76-1.790.21371910.202636453836
1.79-1.810.22731880.189835633751
1.81-1.840.21441900.183736173807
1.84-1.860.17581900.17735953785
1.86-1.890.1841910.165336323823
1.89-1.920.18431920.160936393831
1.92-1.950.16561880.144735853773
1.95-1.980.1571900.139936093799
1.98-2.020.16741910.136936223813
2.02-2.060.15711900.13336163806
2.06-2.10.13811920.125436263818
2.1-2.150.17751910.127836353826
2.15-2.20.1451910.119436423833
2.2-2.250.14631890.122936143803
2.25-2.310.15041910.122936333824
2.31-2.380.12781920.120536393831
2.38-2.460.14421920.12136573849
2.46-2.550.1581920.123636323824
2.55-2.650.15261930.131336673860
2.65-2.770.15571930.132436603853
2.77-2.910.13721930.135536763869
2.91-3.10.16151940.140136763870
3.1-3.340.14041930.137336933886
3.34-3.670.14861950.130237193914
3.67-4.20.14541970.124137493946
4.2-5.290.14781990.124737873986
5.29-47.190.19472110.199939844195
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)
10.7626-0.0473-0.22770.8841-0.1051.05910.03480.03030.0621-0.05940.03360.1231-0.0907-0.1581-0.06120.19690.0217-0.01330.18560.03230.2009-46.5667-4.672-21.3928
20.27330.0454-0.02860.7882-0.23860.50770.0314-0.00960.0012-0.00030.03260.1131-0.0303-0.1207-0.06660.1621-0.00030.00060.20350.01790.1866-45.8418-18.0883-8.2475
30.8676-0.15140.05051.6353-0.16640.8396-0.0477-0.06070.01830.04550.09220.06270.0163-0.0338-0.02710.1578-0.0052-0.00740.1870.01740.1517-38.3692-24.1367-1.6846
40.5475-0.0479-0.04290.3883-0.32040.57670.01840.0153-0.0448-0.09950.00540.06510.1037-0.0628-0.02610.2133-0.0189-0.01770.1704-0.00030.1935-35.2023-31.4156-15.9751
50.2492-0.25920.1281.2412-0.42620.44040.02350.04180.0342-0.1202-0.0405-0.09830.02370.03160.02050.208-0.00540.00960.17450.00860.1995-26.8269-11.7377-26.7082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 421 )A266 - 421
2X-RAY DIFFRACTION2chain 'A' and (resid 422 through 552 )A422 - 552
3X-RAY DIFFRACTION3chain 'A' and (resid 553 through 589 )A553 - 589
4X-RAY DIFFRACTION4chain 'A' and (resid 28 through 121 )A28 - 121
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 265 )A122 - 265

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