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- PDB-7p7y: X-ray structure of Lactobacillus kefir alcohol dehydrogenase muta... -

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Basic information

Entry
Database: PDB / ID: 7p7y
TitleX-ray structure of Lactobacillus kefir alcohol dehydrogenase mutant Q126K
ComponentsNADPH dependent R-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / ketoreductase / R-specific
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP-dependent (R)-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus kefiri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBischoff, D. / Walla, B. / Janowski, R. / Niessing, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1934 Germany
CitationJournal: Crystals / Year: 2021
Title: Transfer of a Rational Crystal Contact Engineering Strategy between Diverse Alcohol Dehydrogenases
Authors: Walla, B. / Bischoff, D. / Janowski, R. / von den Eichen, N. / Niessing, D. / Weuster-Botz, D.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Structure summary / Category: database_2 / entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9557
Polymers27,7111
Non-polymers2446
Water6,197344
1
A: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules

A: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules

A: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules

A: NADPH dependent R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,82028
Polymers110,8454
Non-polymers97524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area17360 Å2
ΔGint-152 kcal/mol
Surface area32330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.840, 80.040, 114.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-303-

MG

21A-410-

HOH

31A-629-

HOH

41A-711-

HOH

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Components

#1: Protein NADPH dependent R-specific alcohol dehydrogenase / NADPH dependent R-specific alcohol dehydrogenase / SDR family NAD(P)-dependent oxidoreductase


Mass: 27711.252 Da / Num. of mol.: 1 / Mutation: Q126K
Source method: isolated from a genetically manipulated source
Details: NADPH dependent R-specific alcohol dehydrogenase / Source: (gene. exp.) Lactobacillus kefiri (bacteria) / Gene: adhR, fabG3, DNL43_05835, LKE01_04370 / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6WVP7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 50 mM Tris/HCl, 25 mM magnesium chloride, 5 % (w/v) PEG 550, 10 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 71194 / % possible obs: 99.2 % / Redundancy: 11.62 % / CC1/2: 1 / Rrim(I) all: 0.033 / Net I/σ(I): 49.61
Reflection shellResolution: 1.25→1.32 Å / Mean I/σ(I) obs: 14.32 / Num. unique obs: 10958 / CC1/2: 0.993 / Rrim(I) all: 0.109 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJan 31, 2020data reduction
XSCALEJan 31, 2020data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7P36

7p36


Resolution: 1.25→45.796 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.12 / WRfactor Rwork: 0.1 / SU B: 0.671 / SU ML: 0.014 / Average fsc free: 0.9835 / Average fsc work: 0.9872 / Cross valid method: FREE R-VALUE / ESU R: 0.027 / ESU R Free: 0.027
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1175 1419 2.001 %
Rwork0.1005 69511 -
all0.101 --
obs-70930 99.347 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 9.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.207 Å2-0 Å2-0 Å2
2--0.792 Å20 Å2
3----0.584 Å2
Refinement stepCycle: LAST / Resolution: 1.25→45.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 12 344 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131971
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171896
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.6412669
X-RAY DIFFRACTIONr_angle_other_deg1.6641.5874387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00723.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7215342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.938159
X-RAY DIFFRACTIONr_chiral_restr0.1120.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022271
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02415
X-RAY DIFFRACTIONr_nbd_refined0.2340.2423
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.21782
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2990
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2956
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.27
X-RAY DIFFRACTIONr_nbd_other0.1810.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.236
X-RAY DIFFRACTIONr_mcbond_it0.8660.7781036
X-RAY DIFFRACTIONr_mcbond_other0.8660.7781035
X-RAY DIFFRACTIONr_mcangle_it1.11.1771306
X-RAY DIFFRACTIONr_mcangle_other1.0991.1771307
X-RAY DIFFRACTIONr_scbond_it1.3470.981935
X-RAY DIFFRACTIONr_scbond_other1.3470.982936
X-RAY DIFFRACTIONr_scangle_it1.6661.3981362
X-RAY DIFFRACTIONr_scangle_other1.6651.3981363
X-RAY DIFFRACTIONr_lrange_it2.33611.5262347
X-RAY DIFFRACTIONr_lrange_other1.90610.42247
X-RAY DIFFRACTIONr_rigid_bond_restr1.87233867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.25-1.2820.144970.09147340.09252190.9750.98492.56560.074
1.282-1.3180.1321000.08849040.08850760.9720.98198.58160.072
1.318-1.3560.097990.07148660.07249650.9880.991000.06
1.356-1.3970.101960.06547190.06548150.9880.9911000.055
1.397-1.4430.094940.06545700.06546640.9880.9911000.057
1.443-1.4940.099900.06344470.06345370.9890.9921000.056
1.494-1.550.086870.06242620.06343490.9910.9921000.056
1.55-1.6130.09840.06341150.06341990.9890.9921000.059
1.613-1.6850.114810.07539660.07540470.9840.9891000.071
1.685-1.7670.131770.08337880.08438650.9810.9871000.08
1.767-1.8630.11750.08736300.08837050.9830.9871000.086
1.863-1.9750.093690.09234080.09234770.9880.9881000.094
1.975-2.1110.1660.09532140.09532810.9870.98899.96950.101
2.111-2.280.098610.09730190.09730800.9880.9881000.104
2.28-2.4970.122570.10627850.10628420.9840.9851000.117
2.497-2.7910.128520.11925370.11925890.980.981000.136
2.791-3.2210.147450.12522170.12622630.970.97899.95580.147
3.221-3.940.115390.13719240.13719630.9760.9811000.16
3.94-5.5510.168310.13415060.13515370.9720.9831000.168
5.551-45.7960.173190.1879000.1879200.9720.9699.89130.228

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