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- PDB-6ow4: Structure of the NADH-bound form of 20beta-Hydroxysteroid Dehydro... -

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Basic information

Entry
Database: PDB / ID: 6ow4
TitleStructure of the NADH-bound form of 20beta-Hydroxysteroid Dehydrogenase from Bifidobacterium adolescentis strain L2-32
ComponentsOxidoreductase, short chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / pyridine nucleotide-dependent enzyme / short-chain dehydrogenase/reductase / NADH dependent
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / nucleotide binding
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, short chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesBifidobacterium adolescentis L2-32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMythen, S.M. / Pollet, R.M. / Koropatkin, N.M. / Ridlon, J.M.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural and biochemical characterization of 20 beta-hydroxysteroid dehydrogenase fromBifidobacterium adolescentisstrain L2-32.
Authors: Doden, H.L. / Pollet, R.M. / Mythen, S.M. / Wawrzak, Z. / Devendran, S. / Cann, I. / Koropatkin, N.M. / Ridlon, J.M.
History
DepositionMay 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
E: Oxidoreductase, short chain dehydrogenase/reductase family protein
F: Oxidoreductase, short chain dehydrogenase/reductase family protein
G: Oxidoreductase, short chain dehydrogenase/reductase family protein
H: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,96716
Polymers253,6598
Non-polymers5,3078
Water8,125451
1
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
E: Oxidoreductase, short chain dehydrogenase/reductase family protein
F: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4838
Polymers126,8304
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25520 Å2
ΔGint-120 kcal/mol
Surface area33550 Å2
MethodPISA
2
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules

C: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules

H: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules

H: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4838
Polymers126,8304
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_547-x+1/2,y-1/2,-z+21
Buried area25490 Å2
ΔGint-125 kcal/mol
Surface area33710 Å2
MethodPISA
3
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
G: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules

D: Oxidoreductase, short chain dehydrogenase/reductase family protein
G: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4838
Polymers126,8304
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area25240 Å2
ΔGint-120 kcal/mol
Surface area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.078, 134.710, 96.396
Angle α, β, γ (deg.)90.00, 100.15, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Oxidoreductase, short chain dehydrogenase/reductase family protein


Mass: 31707.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis L2-32 (bacteria)
Gene: BIFADO_01909 / Production host: Escherichia coli (E. coli) / References: UniProt: A7A7R9
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Mutant S181A 20beta-HSDH purified recombinant protein was incubated with 2.5 mM NADH and 0.25mM or 0.5 mM cortisol for 2 hours at 4C. Crystals were grown in condition 86 of the Hampton ...Details: Mutant S181A 20beta-HSDH purified recombinant protein was incubated with 2.5 mM NADH and 0.25mM or 0.5 mM cortisol for 2 hours at 4C. Crystals were grown in condition 86 of the Hampton PEG/Ion screen containing 0.05 M Citric acid, 0.05 M BIS-TRIS propane / pH 5.0, and 16% w/v Polyethylene glycol 3,350. The condition was then optimized in hanging-drop format using 18-20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.99→103.71 Å / Num. obs: 73226 / % possible obs: 54.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 16.22 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.3
Reflection shellResolution: 1.99→2.045 Å / Num. unique obs: 3662

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M9U

6m9u


Resolution: 1.99→103.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 17.979 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R Free: 0.303 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 3672 5 %RANDOM
Rwork0.18744 ---
obs0.19 69584 51.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.76 Å2
2---0.64 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.99→103.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16825 0 352 451 17628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01317539
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715750
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.66923861
X-RAY DIFFRACTIONr_angle_other_deg1.1251.59236419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62752221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65922.432888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.763152713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.33315109
X-RAY DIFFRACTIONr_chiral_restr0.0360.22357
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219910
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023729
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7762.258902
X-RAY DIFFRACTIONr_mcbond_other0.7762.258901
X-RAY DIFFRACTIONr_mcangle_it1.1733.37111111
X-RAY DIFFRACTIONr_mcangle_other1.1733.37111112
X-RAY DIFFRACTIONr_scbond_it0.7262.48636
X-RAY DIFFRACTIONr_scbond_other0.7262.48637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0413.55312749
X-RAY DIFFRACTIONr_long_range_B_refined2.17326.75619709
X-RAY DIFFRACTIONr_long_range_B_other2.17326.75519710
X-RAY DIFFRACTIONr_rigid_bond_restr0.276333288
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.146 5 -
Rwork0.279 84 -
obs--0.86 %
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)
10.23650.00460.14130.07840.07210.1503-0.00720.0012-0.0051-0.00650.00450.01-0.00340.00560.00270.031-0.0029-0.02020.02970.00050.014529.824866.053826.691
20.3140.04050.11670.17570.03880.1386-0.0099-0.063-0.00750.01730.0142-0.01120.0181-0.033-0.00420.03580.0009-0.01970.05640.00250.012836.293265.278268.5225
30.2499-0.02010.11240.0850.02830.0759-0.02210.0262-0.0026-0.00510.01170.01-0.02140.01810.01030.0402-0.0063-0.02190.03780.00210.013963.339332.294373.7817
40.238-0.07220.1090.1380.04280.1686-0.00990.02520.0079-0.0036-0.00180.0060.0080.01630.01160.02660.0014-0.01530.03590.00040.011561.248898.883574.0768
50.17410.00040.21510.1317-0.02450.27090.01720.037-0.02210.0110.00840.00320.01640.0473-0.02560.02080.0031-0.01830.042-0.00450.017752.164664.362539.2248
60.17910.08040.28650.25730.24430.52380.0334-0.0856-0.0127-0.0241-0.03080.02690.031-0.1188-0.00270.0284-0.0191-0.02510.08150.0060.024613.974360.825655.5492
70.17220.00970.25690.10730.06080.4070.0159-0.0658-0.0023-0.0163-0.00930.00750.0215-0.0937-0.00650.0166-0.0068-0.0150.0586-0.0010.015746.774496.0309103.9585
80.13820.00720.1670.1214-0.04020.2230.00280.0268-0.01340.01320.0061-0.0116-0.00540.0252-0.00890.0255-0.0014-0.02080.0404-0.0020.01782.594696.409987.6078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 294
2X-RAY DIFFRACTION2B21 - 294
3X-RAY DIFFRACTION3C17 - 293
4X-RAY DIFFRACTION4D21 - 294
5X-RAY DIFFRACTION5E11 - 294
6X-RAY DIFFRACTION6F11 - 294
7X-RAY DIFFRACTION7G11 - 294
8X-RAY DIFFRACTION8H12 - 294

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