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- PDB-5gt9: The X-ray structure of 7beta-hydroxysteroid dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 5gt9
TitleThe X-ray structure of 7beta-hydroxysteroid dehydrogenase
ComponentsOxidoreductase, short chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / short chain dehydrogenase / steroid substrates
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 7beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesCollinsella aerofaciens ATCC 25986 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWang, F. / Wang, R. / Lv, Z. / Chen, Q. / Huo, X.
Funding support China, 2items
OrganizationGrant numberCountry
Jiangsu Innovation fund for Technology-based FirmsBC2013062 China
Torch High Technology Industry Development Center, Ministry of Science and Technology, China2015GH581522 China
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of NADP(+)-bound 7 beta-hydroxysteroid dehydrogenase reveals two cofactor-binding modes
Authors: Wang, R. / Wu, J. / Jin, D.K. / Chen, Y. / Lv, Z. / Chen, Q. / Miao, Q. / Huo, X. / Wang, F.
History
DepositionAug 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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)59,0544
Polymers57,5682
Non-polymers1,4872
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-17 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.730, 72.730, 171.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 28783.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Collinsella aerofaciens ATCC 25986 (bacteria)
Strain: ATCC 25986 / Gene: COLAER_02088 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4ECA9
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Sodium malonate pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 51175 / % possible obs: 99.4 % / Redundancy: 6.5 % / Net I/σ(I): 13.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FYD

5fyd


Resolution: 1.7→44.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.953 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2566 5 %RANDOM
Rwork0.165 ---
obs0.167 48520 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 96 202 4317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194244
X-RAY DIFFRACTIONr_bond_other_d0.0010.023965
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.9775756
X-RAY DIFFRACTIONr_angle_other_deg0.84339146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78424.536183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09915718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.521521
X-RAY DIFFRACTIONr_chiral_restr0.1080.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
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_it1.7231.4652110
X-RAY DIFFRACTIONr_mcbond_other1.7211.4642109
X-RAY DIFFRACTIONr_mcangle_it2.4742.192637
X-RAY DIFFRACTIONr_mcangle_other2.4732.1912638
X-RAY DIFFRACTIONr_scbond_it2.9211.8092134
X-RAY DIFFRACTIONr_scbond_other2.9211.8092135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3982.5843114
X-RAY DIFFRACTIONr_long_range_B_refined5.50912.594899
X-RAY DIFFRACTIONr_long_range_B_other5.50612.4614843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 176 -
Rwork0.177 3335 -
obs--94.64 %

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