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- PDB-5fyd: Structural and biochemical insights into 7beta-hydroxysteroid deh... -

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Basic information

Entry
Database: PDB / ID: 5fyd
TitleStructural and biochemical insights into 7beta-hydroxysteroid dehydrogenase stereoselectivity
ComponentsOXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE / STEROID / STEREOSELECTIVITY / DEHYDROGENASE
Function / homology
Function and homology information


bile acid catabolic process / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / lipid catabolic process / nucleotide binding
Similarity search - Function
: / short chain dehydrogenase / 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
7beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCOLLINSELLA AEROFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSavino, S. / Ferrandi, E. / Forneris, F. / Rovida, S. / Riva, S. / Monti, D. / Mattevi, A.
CitationJournal: Proteins / Year: 2016
Title: Structural and Biochemical Insights Into 7Beta-Hydroxysteroid Dehydrogenase Stereoselectivity.
Authors: Savino, S. / Ferrandi, E.E. / Forneris, F. / Rovida, S. / Riva, S. / Monti, D. / Mattevi, A.
History
DepositionMar 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)57,6603
Polymers57,5682
Non-polymers921
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-13.9 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.770, 83.040, 47.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2030-

HOH

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Components

#1: Protein OXIDOREDUCTASE, SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY PROTEIN / 7BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 28783.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COLLINSELLA AEROFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4ECA9, 7beta-hydroxysteroid dehydrogenase (NADP+)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 345 / 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: 1.98 Å3/Da / Density % sol: 37 % / Description: NONE
Crystal growpH: 4.6
Details: 1 M SODIUM FORMATE, 100 MM SODIUM ACETATE PH 4.6, ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97795
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 1.6→24.6 Å / Num. obs: 61266 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AHH

1ahh


Resolution: 1.6→67.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.24 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20882 3005 4.9 %RANDOM
Rwork0.17614 ---
obs0.17775 58202 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.287 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.38 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→67.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 6 345 4243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194000
X-RAY DIFFRACTIONr_bond_other_d0.0020.023773
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9485404
X-RAY DIFFRACTIONr_angle_other_deg0.93138704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49424.798173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34415685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02889
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_it1.3191.922058
X-RAY DIFFRACTIONr_mcbond_other1.3021.9192057
X-RAY DIFFRACTIONr_mcangle_it2.1522.872573
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9772.1971941
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 215 -
Rwork0.312 4233 -
obs--99.96 %

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