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- PDB-5epo: The three-dimensional structure of Clostridium absonum 7alpha-hyd... -

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Basic information

Entry
Database: PDB / ID: 5epo
TitleThe three-dimensional structure of Clostridium absonum 7alpha-hydroxysteroid dehydrogenase
Components7-alpha-hydroxysteroid deydrogenase
KeywordsOXIDOREDUCTASE / Oxidoreductase Activity / Metabolic Process
Function / homology
Function and homology information


bile acid catabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / lipid catabolic process / oxidoreductase activity / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TAUROCHENODEOXYCHOLIC ACID / 7alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesClostridium sardiniense (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLou, D. / Wang, B. / Wang, F.
Funding support China, 1items
OrganizationGrant numberCountry
2014ZX09301306-007 China
CitationJournal: Sci Rep / Year: 2016
Title: The three-dimensional structure of Clostridium absonum 7 alpha-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP(H) recognition
Authors: Lou, D. / Wang, B. / Tan, J. / Zhu, L. / Cen, X. / Ji, Q. / Wang, Y.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7-alpha-hydroxysteroid deydrogenase
B: 7-alpha-hydroxysteroid deydrogenase
C: 7-alpha-hydroxysteroid deydrogenase
D: 7-alpha-hydroxysteroid deydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,62116
Polymers113,2804
Non-polymers5,34112
Water17,925995
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26610 Å2
ΔGint-136 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.180, 69.680, 220.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
7-alpha-hydroxysteroid deydrogenase


Mass: 28320.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium sardiniense (bacteria) / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G9FRD7
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-TUD / TAUROCHENODEOXYCHOLIC ACID / 2-(((3ALPHA,5BETA,7ALPHA)-3,7-DIHYDROXY-24-OXOCHOLAN-24-YL)AMINO)ETHANESULFONIC ACID / TAUROCHENODEOXYCHOLATE


Mass: 499.704 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H45NO6S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 995 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0M Ammonium citrate tribasic, 0.1M BIS-TRIS propane, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.726→110.195 Å / Num. obs: 69768 / % possible obs: 98.3 % / Redundancy: 6.7 % / Net I/σ(I): 7.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALAdata scaling
PHASERphasing
RefinementResolution: 2→49.58 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.008 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22189 3540 5.1 %RANDOM
Rwork0.1821 ---
obs0.18411 66141 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7914 0 352 995 9261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198414
X-RAY DIFFRACTIONr_bond_other_d0.0030.028049
X-RAY DIFFRACTIONr_angle_refined_deg1.5652.01711452
X-RAY DIFFRACTIONr_angle_other_deg1.082318498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39651041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6624.197355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.603151359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6161559
X-RAY DIFFRACTIONr_chiral_restr0.0850.21325
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029390
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021837
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_it1.1961.2334176
X-RAY DIFFRACTIONr_mcbond_other1.1951.2324175
X-RAY DIFFRACTIONr_mcangle_it1.8711.8395213
X-RAY DIFFRACTIONr_mcangle_other1.8711.845214
X-RAY DIFFRACTIONr_scbond_it2.7031.7024238
X-RAY DIFFRACTIONr_scbond_other2.7031.7024238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3282.4266240
X-RAY DIFFRACTIONr_long_range_B_refined6.64512.8637181
X-RAY DIFFRACTIONr_long_range_B_other6.45812.49836100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 222 -
Rwork0.273 4057 -
obs--82.13 %

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