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- PDB-6gsd: Plantago Major multifunctional oxidoreductase in complex with pro... -

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Basic information

Entry
Database: PDB / ID: 6gsd
TitlePlantago Major multifunctional oxidoreductase in complex with progesterone and NADP+
ComponentsProgesterone 5-beta-reductase
KeywordsOXIDOREDUCTASE / Progesterone Reductase / Iridoid synthase / SDR / enzyme evolution
Function / homology
Function and homology information


3beta-hydroxy-Delta5-steroid dehydrogenase / 3-beta-hydroxy-Delta5-steroid dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-CH group of donors / nucleotide binding
Similarity search - Function
: / PRISE-like Rossmann-fold domain / 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 / PROGESTERONE / Progesterone 5-beta-reductase
Similarity search - Component
Biological speciesPlantago major (common plantain)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFellows, R. / Silva, C. / Russo, C.M. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M.
CitationJournal: Sci Rep / Year: 2018
Title: A multisubstrate reductase from Plantago major: structure-function in the short chain reductase superfamily.
Authors: Fellows, R. / Russo, C.M. / Silva, C.S. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M.H.
History
DepositionJun 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Progesterone 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0923
Polymers44,1141
Non-polymers9782
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-0 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.839, 78.839, 134.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Progesterone 5-beta-reductase


Mass: 44113.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plantago major (common plantain) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D6N9X1, 3beta-hydroxy-Delta5-steroid dehydrogenase
#2: Chemical ChemComp-STR / PROGESTERONE


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis Tris Propane, 5% glycerol, and 16.5% to 19% Peg 5K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 25, 2018 / Details: MIRROR and CRLs
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.59→68 Å / Num. obs: 13258 / % possible obs: 95 % / Redundancy: 7.6 % / CC1/2: 0.91 / Rrim(I) all: 0.092 / Net I/σ(I): 14.3
Reflection shellResolution: 2.59→2.65 Å / Mean I/σ(I) obs: 1 / CC1/2: 0.27

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSJune 1 2017data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6F

2v6f


Resolution: 2.7→39.419 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.33 / Phase error: 28.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 552 4.72 %RANDOM
Rwork0.2054 ---
obs0.2082 11705 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 67 26 3004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0263076
X-RAY DIFFRACTIONf_angle_d1.364200
X-RAY DIFFRACTIONf_dihedral_angle_d15.5451783
X-RAY DIFFRACTIONf_chiral_restr0.723450
X-RAY DIFFRACTIONf_plane_restr0.005532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.97170.34411360.28832727X-RAY DIFFRACTION97
2.9717-3.40150.31321430.2582757X-RAY DIFFRACTION96
3.4015-4.28470.2741310.19052788X-RAY DIFFRACTION96
4.2847-39.42370.23711420.18922881X-RAY DIFFRACTION94
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)
10.6783-0.58430.45080.5647-0.25450.5253-0.2342-0.4651-0.64240.3722-0.0169-0.1364-0.41590.6257-0.00010.7685-0.1030.03790.8436-0.1030.6796-15.8931-2.865325.3129
22.97150.345-0.11431.68530.21151.7108-0.0133-0.34270.23460.26790.11070.2195-0.2561-0.3552-00.62060.06020.07590.6496-0.0330.6448-31.7911-3.067816.0686
31.1805-0.3231-0.70140.4921-0.25151.9235-0.1172-0.1258-0.2881-0.37110.04640.1420.3612-0.1293-00.5699-0.0778-0.00480.60630.04380.6687-22.0228-24.493214.59
41.1805-0.3079-0.03990.87870.54030.80330.0867-0.4269-0.13510.07480.17320.23320.272-0.18140.00020.5412-0.07520.00680.74750.08080.6195-21.9296-22.751121.6774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 26:79)
2X-RAY DIFFRACTION2(chain A and resseq 80:214)
3X-RAY DIFFRACTION3(chain A and resseq 215:308)
4X-RAY DIFFRACTION4(chain A and resseq 309:389)

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