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- PDB-2v6f: Structure of Progesterone 5beta-Reductase from Digitalis Lanata -

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Basic information

Entry
Database: PDB / ID: 2v6f
TitleStructure of Progesterone 5beta-Reductase from Digitalis Lanata
ComponentsPROGESTERONE 5-BETA-REDUCTASE
KeywordsOXIDOREDUCTASE / TYROSINE-DEPENDENT OXIDOREDUCTASE / SDR / REDUCTASE / CARDENOLIDES / CARDIAC GLYCOSIDES
Function / homology
Function and homology information


Delta4-3-oxosteroid 5beta-reductase / Delta4-3-oxosteroid 5beta-reductase activity / nucleotide binding
Similarity search - Function
: / PRISE-like Rossmann-fold domain / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxo-Delta(4,5)-steroid 5-beta-reductase
Similarity search - Component
Biological speciesDIGITALIS LANATA (wooly foxglove)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsThorn, A. / Egerer-Sieber, C. / Jaeger, C.M. / Herl, V. / Mueller-Uri, F. / Kreis, W. / Muller, Y.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Crystal Structure of Progesterone 5{Beta}-Reductase from Digitalis Lanata Defines a Novel Class of Short Chain Dehydrogenases/Reductases.
Authors: Thorn, A. / Egerer-Sieber, C. / Jaeger, C.M. / Herl, V. / Mueller-Uri, F. / Kreis, W. / Muller, Y.A.
History
DepositionJul 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)41,3512
Polymers41,3281
Non-polymers231
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.660, 78.660, 180.990
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: 41327.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DIGITALIS LANATA (wooly foxglove) / Organ: LEAVES / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: Q6PQJ9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAT POSITION 298 GLUTAMIC ACID INSTEAD OF GLYCINE. (INITIAL SEQUENCING ERROR)

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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: 3.4 Å3/Da / Density % sol: 63.8 % / Description: NONE
Crystal growpH: 5.6
Details: 1 MICROL OF PROTEIN SOLUTION WAS MIXED WITH 1 MICROL OF RESERVOIR SOLUTION (15 % PEG 4000, 0.1 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.6) AND THE DROPLET SUSPENDED OVER 700 ML OF RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 23196 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 18.9 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.7
Reflection shellResolution: 2.4→2.56 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.4→39.34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 16.477 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2304 10 %RANDOM
Rwork0.205 ---
obs0.21 20737 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.51 Å20 Å20 Å2
2--5.51 Å20 Å2
3----11.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 1 139 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222864
X-RAY DIFFRACTIONr_bond_other_d0.0040.021904
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9413892
X-RAY DIFFRACTIONr_angle_other_deg0.96834639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95724.737133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63915455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.551510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_nbd_refined0.2090.2601
X-RAY DIFFRACTIONr_nbd_other0.1840.21904
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21366
X-RAY DIFFRACTIONr_nbtor_other0.090.21420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5341.51760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95522829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43931169
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.114.51063
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 166
Rwork0.306 1499
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)
12.72971.22320.64083.38290.47114.09760.1484-0.2009-0.35710.0806-0.23490.40440.7078-1.01250.0865-0.3211-0.1751-0.0355-0.1768-0.02550.4456-0.636-30.52142.27
22.95520.32143.89190.59941.10587.2019-0.2846-0.21010.2763-0.3107-0.19310.311-0.6652-0.72660.4777-0.27230.1095-0.0823-0.2878-0.05650.4771-3.476-11.21324.502
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 208
2X-RAY DIFFRACTION1A250 - 279
3X-RAY DIFFRACTION1A353 - 368
4X-RAY DIFFRACTION2A209 - 249
5X-RAY DIFFRACTION2A280 - 352
6X-RAY DIFFRACTION2A369 - 389

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