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- PDB-6el3: Structure of Progesterone 5beta-Reductase from Arabidopsis thalia... -

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Basic information

Entry
Database: PDB / ID: 6el3
TitleStructure of Progesterone 5beta-Reductase from Arabidopsis thaliana in complex with NADP
Components(3-oxo-Delta(4,5)-steroid 5-beta- ...) x 6
KeywordsOXIDOREDUCTASE / short chain dehydrogenase/reductase (SDR) fold / homodimer / NADP binding site
Function / homology
Function and homology information


enone reductase activity / xylem and phloem pattern formation / Delta4-3-oxosteroid 5beta-reductase / Delta4-3-oxosteroid 5beta-reductase activity / steroid metabolic process / response to wounding / protein dimerization activity / cytosol
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxo-Delta(4,5)-steroid 5-beta-reductase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsMuller, Y.A. / Schmidt, K. / Egerer-Sieber, C.
CitationJournal: Phytochemistry / Year: 2018
Title: PRISEs (progesterone 5 beta-reductase and/or iridoid synthase-like 1,4-enone reductases): Catalytic and substrate promiscuity allows for realization of multiple pathways in plant metabolism.
Authors: Schmidt, K. / Petersen, J. / Munkert, J. / Egerer-Sieber, C. / Hornig, M. / Muller, Y.A. / Kreis, W.
History
DepositionSep 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
B: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
C: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
D: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
E: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
F: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,90118
Polymers264,2286
Non-polymers4,67312
Water48,1542673
1
C: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
D: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6166
Polymers88,0582
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-47 kcal/mol
Surface area29160 Å2
MethodPISA
2
E: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
F: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5896
Polymers88,0312
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-48 kcal/mol
Surface area28990 Å2
MethodPISA
3
A: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
B: 3-oxo-Delta(4,5)-steroid 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6976
Polymers88,1392
Non-polymers1,5584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-47 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.460, 94.860, 313.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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3-oxo-Delta(4,5)-steroid 5-beta- ... , 6 types, 6 molecules ABCDEF

#1: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44055.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#2: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44083.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#3: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44055.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#4: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44001.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#5: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 44055.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase
#6: Protein 3-oxo-Delta(4,5)-steroid 5-beta-reductase / Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / ...Delta(4)-3-oxosteroid 5-beta-reductase / Delta-4 / 5-steroid 5-beta-reductase / At5beta-StR / Progesterone 5-beta-reductase / 5beta-POR / Protein VEIN PATTERNING 1


Mass: 43974.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: -N-terminal residues were not modelled due to missing electron density -Dimethyllysines were only built where electron density was unambiguous
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: VEP1, AWI31, At4g24220, T22A6.50 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9STX2, Delta4-3-oxosteroid 5beta-reductase

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Non-polymers , 3 types, 2685 molecules

#7: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2673 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.4 M sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.899→47.43 Å / Num. obs: 217162 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rrim(I) all: 0.169 / Net I/σ(I): 9.35
Reflection shellResolution: 1.899→2.01 Å / Redundancy: 6.9 % / Num. unique obs: 34610 / CC1/2: 0.731 / Rrim(I) all: 0.93 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6G

2v6g


Resolution: 1.899→46.896 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.2128 2280 1.05 %
Rwork0.1675 --
obs0.168 217118 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.899→46.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17740 0 294 2673 20707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818594
X-RAY DIFFRACTIONf_angle_d1.125350
X-RAY DIFFRACTIONf_dihedral_angle_d21.1626728
X-RAY DIFFRACTIONf_chiral_restr0.6082647
X-RAY DIFFRACTIONf_plane_restr0.0053206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.94030.28781390.236213094X-RAY DIFFRACTION98
1.9403-1.98550.26491410.217913254X-RAY DIFFRACTION100
1.9855-2.03510.22191420.205213374X-RAY DIFFRACTION100
2.0351-2.09010.25031410.194313287X-RAY DIFFRACTION100
2.0901-2.15170.24871420.19213361X-RAY DIFFRACTION100
2.1517-2.22110.22751410.180413323X-RAY DIFFRACTION100
2.2211-2.30050.23111420.178613339X-RAY DIFFRACTION100
2.3005-2.39260.21361420.170113387X-RAY DIFFRACTION100
2.3926-2.50150.19171420.168813420X-RAY DIFFRACTION100
2.5015-2.63330.22411420.172713403X-RAY DIFFRACTION100
2.6333-2.79830.24671430.176813434X-RAY DIFFRACTION100
2.7983-3.01430.22411420.182213426X-RAY DIFFRACTION100
3.0143-3.31760.23081430.169413480X-RAY DIFFRACTION100
3.3176-3.79750.18281430.151213566X-RAY DIFFRACTION100
3.7975-4.78370.15921450.130513651X-RAY DIFFRACTION100
4.7837-46.91070.20491500.148414039X-RAY DIFFRACTION99

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