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- PDB-2v6g: Structure of Progesterone 5beta-Reductase from Digitalis Lanata i... -

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Basic information

Entry
Database: PDB / ID: 2v6g
TitleStructure of Progesterone 5beta-Reductase from Digitalis Lanata in complex with NADP
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxo-Delta(4,5)-steroid 5-beta-reductase
Similarity search - Component
Biological speciesDIGITALIS LANATA (wooly foxglove)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThorn, A. / Egerer-Sieber, C. / Jaeger, C. / 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. / 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 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)42,1304
Polymers41,3281
Non-polymers8023
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.590, 78.590, 178.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1087-

HOH

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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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.3 Å3/Da / Density % sol: 63.2 % / Description: NONE
Crystal growpH: 5.8
Details: CONTAINERLESS BATCH METHOD: 300 MICROL OF HIGH-DENSITY SILICON OIL WAS TRANSFERRED INTO A WELL OF A CELL CULTURE PLATE AND OVER-LAID WITH 500 MICROL OF REGULAR SILICON OIL. AT THE INTERFACE ...Details: CONTAINERLESS BATCH METHOD: 300 MICROL OF HIGH-DENSITY SILICON OIL WAS TRANSFERRED INTO A WELL OF A CELL CULTURE PLATE AND OVER-LAID WITH 500 MICROL OF REGULAR SILICON OIL. AT THE INTERFACE BETWEEN THE TWO LIQUIDS A DROPLET WAS DEPOSITED THAT WAS OBTAINED BY MIXING 0.4 MICROL OF H2O, 2.2 MICROL OF 5BETA-POR SOLUTION WITH NADP AND PROGESTERONE ADDED AND 1.8 MICROL OF A CRYSTALLIZATION SOLUTION CONSISTING OF 22.9 % MPD, 3.5 % PEG 8000, 0.05 M SODIUM ACETATE, 0.02 M CACL2, PH 5.8.

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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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 25629 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 14.3 % / Biso Wilson estimate: 49.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NADP FREE STRUCTURE

Resolution: 2.3→39.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.818 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2557 10 %RANDOM
Rwork0.171 ---
obs0.175 23072 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: 39.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 50 157 3096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223023
X-RAY DIFFRACTIONr_bond_other_d0.0030.022008
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.964119
X-RAY DIFFRACTIONr_angle_other_deg0.99634896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1675363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32824.681141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91315480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861511
X-RAY DIFFRACTIONr_chiral_restr0.1410.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023357
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
X-RAY DIFFRACTIONr_nbd_refined0.2010.2571
X-RAY DIFFRACTIONr_nbd_other0.1810.21978
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21414
X-RAY DIFFRACTIONr_nbtor_other0.0870.21473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4731.51812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86222922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41531286
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0954.51197
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 177
Rwork0.22 1680
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)
13.00020.95180.83093.04560.50813.63330.0694-0.1617-0.33680.0819-0.1640.39410.5726-0.90780.0945-0.0454-0.12350.00180.1444-0.0358-0.2575-1.188-29.94641.146
23.71830.28472.80051.52071.29366.8468-0.3615-0.07090.453-0.2415-0.08390.2381-0.6258-0.54920.4454-0.03440.0987-0.11120.0025-0.0417-0.2766-3.655-11.02123.913
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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