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- PDB-6m9u: Structure of the apo-form of 20beta-Hydroxysteroid Dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 6m9u
TitleStructure of the apo-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
IMIDAZOLE / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Oxidoreductase, short chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesBifidobacterium adolescentis L2-32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionAug 24, 2018Deposition 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,79836
Polymers61,0442
Non-polymers2,75434
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint49 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.371, 168.371, 126.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-315-

IMD

21B-316-

IMD

31B-316-

IMD

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 30522.064 Da / Num. of mol.: 2
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

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Non-polymers , 9 types, 194 molecules

#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.69 Å3/Da / Density % sol: 70.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% v/v 2-propanol, 0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50.69 Å / Num. obs: 338597 / % possible obs: 99.57 % / Redundancy: 7.3 % / Biso Wilson estimate: 41.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1402 / Rpim(I) all: 0.05497 / Rrim(I) all: 0.1509 / Net I/σ(I): 9.52
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 33468 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R1I

3r1i


Resolution: 2.2→50.686 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.11
RfactorNum. reflection% reflection
Rfree0.2311 3804 4.34 %
Rwork0.1959 --
obs0.1974 87657 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 232.73 Å2 / Biso mean: 65.9959 Å2 / Biso min: 27.37 Å2
Refinement stepCycle: final / Resolution: 2.2→50.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 436 160 4403
Biso mean--92.43 59.5 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.22790.40521390.39713086322598
2.2279-2.25720.41041450.37433095324098
2.2572-2.28810.39531390.36723081322098
2.2881-2.32080.40981350.35053081321698
2.3208-2.35540.32411380.34713054319298
2.3554-2.39220.32441390.3323049318898
2.3922-2.43150.33911390.32023100323999
2.4315-2.47340.35111420.30783061320398
2.4734-2.51840.31971420.30783109325198
2.5184-2.56680.34941420.27233109325199
2.5668-2.61920.2731410.26953087322899
2.6192-2.67610.31181460.25413111325799
2.6761-2.73840.27951390.2353121326099
2.7384-2.80690.25471420.21483148329099
2.8069-2.88280.24921390.20283082322199
2.8828-2.96760.21471450.1913127327299
2.9676-3.06330.25621330.18053114324799
3.0633-3.17280.22371430.17583137328099
3.1728-3.29980.2171440.174831153259100
3.2998-3.450.19461430.163631243267100
3.45-3.63180.20411420.146731193261100
3.6318-3.85930.16421430.144531363279100
3.8593-4.15710.19731360.14243103323999
4.1571-4.57520.16811400.13253118325899
4.5752-5.23670.15641410.148931353276100
5.2367-6.59540.2271430.192331363279100
6.5954-50.6990.22821440.1953115325999

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