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- PDB-5mlh: Plantago Major multifunctional oxidoreductase in complex with 8-o... -

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Basic information

Entry
Database: PDB / ID: 5mlh
TitlePlantago Major multifunctional oxidoreductase in complex with 8-oxogeranial 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 / lipid metabolic process / 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 / (2E,6E)-2,6-dimethylocta-2,6-dienedial / Progesterone 5-beta-reductase
Similarity search - Component
Biological speciesPlantago major (common plantain)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsFellows, R. / Russo, C.M. / Lee, S.G. / Jez, J.M. / Chisholm, J.D. / Zubieta, C. / Nanao, M.
Funding support France, 2items
OrganizationGrant numberCountry
BioStructXN283570 France
French National Research AgencyATIP Chloe Zubieta France
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 6, 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,1796
Polymers44,1141
Non-polymers1,0655
Water3,459192
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-29 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.520, 79.520, 138.200
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-535-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 197 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-XOG / (2E,6E)-2,6-dimethylocta-2,6-dienedial / 8-oxogeranial


Mass: 166.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
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: Mar 29, 2013 / Details: KB
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 38252 / % possible obs: 99.7 % / Redundancy: 12.88 % / Biso Wilson estimate: 39.49 Å2 / Net I/σ(I): 27.38
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 10.98 % / Mean I/σ(I) obs: 1.71 / Num. measured obs: 42619 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6F

2v6f


Resolution: 1.86→39.86 Å / Cor.coef. Fo:Fc: 0.9685 / Cor.coef. Fo:Fc free: 0.9556 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.125 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1698 5.01 %RANDOM
Rwork0.1602 ---
obs0.1624 33919 89.25 %-
Displacement parametersBiso mean: 49.31 Å2
Baniso -1Baniso -2Baniso -3
1--3.0186 Å20 Å20 Å2
2---3.0186 Å20 Å2
3---6.0372 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: 1 / Resolution: 1.86→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 68 192 3203
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0153102HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.184234HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1066SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes469HARMONIC5
X-RAY DIFFRACTIONt_it3102HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.06
X-RAY DIFFRACTIONt_other_torsion18.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion389SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3760SEMIHARMONIC4
LS refinement shellResolution: 1.86→1.92 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2873 140 5.55 %
Rwork0.2586 2383 -
all0.2602 2523 -
obs--77.96 %
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)
13.0691.0433-0.64352.7957-1.22864.9395-0.1098-0.41940.29320.3120.0873-0.237-0.53580.53660.0225-0.0208-0.0834-0.0265-0.0045-0.0823-0.0809-16.3766-3.192623.8839
21.94260.580.17112.4385-0.22082.45450.0584-0.51180.34470.3675-0.03720.1112-0.5442-0.1705-0.02120.04640.03080.0469-0.083-0.1006-0.0976-28.58711.125423.787
32.3806-0.0382-0.01951.0450.13083.15180.0134-0.03220.1366-0.16270.02130.0643-0.3993-0.3803-0.0346-0.0850.04090.02-0.00240.014-0.0174-36.7419-7.82548.3279
41.2685-0.0038-0.16081.138-0.43752.2492-0.0267-0.1772-0.08880.0350.05810.1221-0.0202-0.071-0.0314-0.1366-0.03350.0115-0.04910.0115-0.039-22.7154-18.56614.2901
53.8551.28890.38622.5843-1.48720.7486-0.0438-0.5442-0.54420.14230.22810.13590.5442-0.343-0.1843-0.1053-0.10620.00820.03160.1520.0181-24.9166-34.004126.1054
61.4887-0.24960.0270.8039-0.53772.1803-0.0164-0.3177-0.09670.06550.07850.0419-0.1288-0.0455-0.0621-0.0924-0.0170.0118-0.0220.0106-0.018-20.8811-20.24817.9182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|26 - 69}
2X-RAY DIFFRACTION2{A|70 - 145}
3X-RAY DIFFRACTION3{A|146 - 194}
4X-RAY DIFFRACTION4{A|195 - 287}
5X-RAY DIFFRACTION5{A|288 - 327}
6X-RAY DIFFRACTION6{A|328 - 389}

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