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- PDB-5mlm: Plantago Major multifunctional oxidoreductase V150M mutant in com... -

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Basic information

Entry
Database: PDB / ID: 5mlm
TitlePlantago Major multifunctional oxidoreductase V150M mutant 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PROGESTERONE / Progesterone 5-beta-reductase
Similarity search - Component
Biological speciesPlantago major (common plantain)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.563 Å
AuthorsFellows, R. / 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
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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 / _citation.year / _entity.formula_weight
Revision 1.2Mar 6, 2019Group: Data collection / Structure summary / Category: entity / reflns / Item: _entity.formula_weight / _reflns.pdbx_Rmerge_I_obs
Revision 1.3Jan 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,8793
Polymers46,8211
Non-polymers1,0582
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-0 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.288, 78.288, 135.869
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: 46820.832 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 / Comment: hormone*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis Tris Propane, 5% glycerol, 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: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 23, 2014 / Details: KB
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 25539 / % possible obs: 96.7 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.91
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
5.51-504.30.02542.70.999199.4
2.56-2.652.930.8171.470.695171.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2v6f

2v6f


Resolution: 2.563→42.914 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.2577 700 5.05 %
Rwork0.1775 --
obs0.1816 13861 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.563→42.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 71 60 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083074
X-RAY DIFFRACTIONf_angle_d1.0064196
X-RAY DIFFRACTIONf_dihedral_angle_d13.2411830
X-RAY DIFFRACTIONf_chiral_restr0.053445
X-RAY DIFFRACTIONf_plane_restr0.007557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.563-2.76090.37671220.30972340X-RAY DIFFRACTION89
2.7609-3.03870.3191440.2562635X-RAY DIFFRACTION100
3.0387-3.47820.30631190.20522663X-RAY DIFFRACTION100
3.4782-4.38150.21831520.15042691X-RAY DIFFRACTION100
4.3815-42.92020.23991630.14752832X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -25.0082 Å / Origin y: -12.6499 Å / Origin z: 18.1842 Å
111213212223313233
T0.3336 Å2-0.0722 Å20.0418 Å2-0.6734 Å2-0.1681 Å2--0.5213 Å2
L1.9511 °2-0.4334 °20.4872 °2-1.5593 °2-0.3743 °2--2.718 °2
S-0.021 Å °-0.7105 Å °0.1583 Å °0.1943 Å °0.008 Å °0.0233 Å °-0.3175 Å °-0.4536 Å °-0.0028 Å °
Refinement TLS groupSelection details: (chain A and resseq 26:389)

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