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- PDB-7p36: X-ray structure of Lactobacillus kefir alcohol dehydrogenase (wil... -

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Basic information

Entry
Database: PDB / ID: 7p36
TitleX-ray structure of Lactobacillus kefir alcohol dehydrogenase (wild type)
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: 1.14 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 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,0438
Polymers27,7101
Non-polymers3327
Water6,972387
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)112,17032
Polymers110,8414
Non-polymers1,32928
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 area18270 Å2
ΔGint-110 kcal/mol
Surface area32110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.870, 79.970, 114.590
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-301-

MG

21A-416-

HOH

31A-739-

HOH

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Components

#1: Protein NADPH dependent R-specific alcohol dehydrogenase / 3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase / NADPH dependent R-specific alcohol ...3-alpha-(Or 20-beta)-hydroxysteroid dehydrogenase / NADPH dependent R-specific alcohol dehydrogenase / SDR family NAD(P)-dependent oxidoreductase


Mass: 27710.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 50 mM Tris/HCl, 25 mM magnesium chloride, 5 % (w/v) PEG 3000, 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: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.14→45.8 Å / Num. obs: 93534 / % possible obs: 100 % / Redundancy: 12.81 % / CC1/2: 1 / Rrim(I) all: 0.023 / Net I/σ(I): 71.35
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 11.99 % / Mean I/σ(I) obs: 26.89 / Num. unique obs: 14945 / CC1/2: 0.998 / Rrim(I) all: 0.083 / % possible all: 99.8

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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: 4RF4

4rf4


Resolution: 1.14→45.8 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / WRfactor Rfree: 0.105 / WRfactor Rwork: 0.092 / SU B: 0.439 / SU ML: 0.01 / Average fsc free: 0.9874 / Average fsc work: 0.9899 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.02
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1072 4675 5.001 %
Rwork0.0931 88811 -
all0.094 --
obs-93486 99.991 %
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: 8.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.074 Å20 Å20 Å2
2---0.093 Å20 Å2
3---0.019 Å2
Refinement stepCycle: LAST / Resolution: 1.14→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 19 387 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171966
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.6442788
X-RAY DIFFRACTIONr_angle_other_deg1.6771.5874553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68523.3792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2915356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5481510
X-RAY DIFFRACTIONr_chiral_restr0.110.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022406
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02438
X-RAY DIFFRACTIONr_nbd_refined0.2320.2467
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.21865
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21026
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.213
X-RAY DIFFRACTIONr_nbd_other0.2180.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.248
X-RAY DIFFRACTIONr_mcbond_it0.7690.6321075
X-RAY DIFFRACTIONr_mcbond_other0.7690.6321074
X-RAY DIFFRACTIONr_mcangle_it0.9030.9591367
X-RAY DIFFRACTIONr_mcangle_other0.9030.9591368
X-RAY DIFFRACTIONr_scbond_it1.1590.803978
X-RAY DIFFRACTIONr_scbond_other1.1590.804979
X-RAY DIFFRACTIONr_scangle_it1.4531.1431420
X-RAY DIFFRACTIONr_scangle_other1.4531.1441421
X-RAY DIFFRACTIONr_lrange_it2.90210.0972502
X-RAY DIFFRACTIONr_lrange_other2.328.7782379
X-RAY DIFFRACTIONr_rigid_bond_restr2.00534019
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
1.14-1.170.1283400.09664580.09868010.9770.98399.95590.075
1.17-1.2020.0893340.07663430.07766780.9870.98999.9850.061
1.202-1.2360.0873270.07162050.07265320.990.9911000.057
1.236-1.2740.0883140.06659820.06762960.9910.9931000.055
1.274-1.3160.0843060.06858090.06961150.9910.9931000.057
1.316-1.3620.0912960.06856260.06959220.990.9921000.059
1.362-1.4140.0832860.06554380.06657240.9910.9931000.057
1.414-1.4710.0892770.06852500.06955270.9910.9931000.06
1.471-1.5370.0832650.06750400.06753050.9910.9931000.06
1.537-1.6120.0882510.06847780.06950290.9910.9931000.063
1.612-1.6990.0982430.07746050.07848480.9880.9911000.073
1.699-1.8020.0972280.08243370.08345650.9890.9911000.079
1.802-1.9260.0952160.08841030.08843190.9890.991000.086
1.926-2.080.0932010.09138170.09140180.990.9911000.093
2.08-2.2780.0931850.09335170.09337020.990.9891000.097
2.278-2.5460.1191690.10532070.10533760.9850.9871000.113
2.546-2.9380.1331490.11428370.11529860.9790.9851000.128
2.938-3.5950.1261280.12124230.12125510.9820.9831000.139
3.595-5.0690.1411000.12619100.12620100.980.9831000.149
5.069-45.80.21600.19311270.19411880.9390.96399.91580.232

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