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

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Basic information

Entry
Database: PDB / ID: 5mlr
TitlePlantago Major multifunctional oxidoreductase V150M mutant in complex with citral 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 / cholesterol dehydrogenase activity / 3-beta-hydroxy-delta5-steroid dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors / lipid metabolic process
Similarity search - Function
NAD-dependent epimerase/dehydratase / 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
Geranaldehyde / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Progesterone 5-beta-reductase
Similarity search - Component
Biological speciesPlantago major (common plantain)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 1.2Jan 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)47,9507
Polymers46,8211
Non-polymers1,1296
Water9,458525
1
A: Progesterone 5-beta-reductase
hetero molecules

A: Progesterone 5-beta-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,90014
Polymers93,6422
Non-polymers2,25912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5400 Å2
ΔGint-88 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.510, 79.510, 137.613
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-539-

HOH

21A-1011-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 531 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GRQ / Geranaldehyde / Citral


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis Tris Propane, 5% glycerol, and 16.5%-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: Jan 25, 2014
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 76281 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.9
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 5.87 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 1.53 / CC1/2: 0.56 / % possible all: 88.6

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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: 1.46→29.2 Å / Cor.coef. Fo:Fc: 0.9702 / Cor.coef. Fo:Fc free: 0.9641 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.059 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.053
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 3834 5.03 %RANDOM
Rwork0.1526 ---
obs0.1534 76267 98.85 %-
Displacement parametersBiso mean: 26.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.4654 Å20 Å20 Å2
2---1.4654 Å20 Å2
3---2.9307 Å2
Refine analyzeLuzzati coordinate error obs: 0.159 Å
Refinement stepCycle: 1 / Resolution: 1.46→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 73 525 3552
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013120HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14262HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1080SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it3120HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.39
X-RAY DIFFRACTIONt_other_torsion15.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion391SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies9HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4148SEMIHARMONIC4
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2437 213 4.44 %
Rwork0.2299 4586 -
all0.2305 4799 -
obs--85.19 %
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)
10.87920.04480.16780.5441-0.02571.2461-0.0277-0.15450.11280.0860.0163-0.0076-0.312-0.07840.0114-0.00440.00820.0081-0.0404-0.0259-0.0522-27.9988-3.54519.2701
20.7613-0.48840.70481.12150.3520.5360.0051-0.01640.0719-0.0047-0.0136-0.0312-0.077-0.06690.00850.23030.07140.0302-0.0895-0.0252-0.0242-31.841911.723512.2749
30.7201-0.0730.11310.5557-0.0360.8952-0.0035-0.0959-0.0712-0.0020.02140.0049-0.0228-0.0384-0.018-0.0657-0.02210.0054-0.03250.0047-0.0309-21.9663-20.431514.9695
40.266-0.9813-0.16280.30930.96650.646-0.0204-0.0695-0.1417-0.04760.04830.04590.0408-0.1588-0.0279-0.02-0.1343-0.00330.0380.05590.0544-32.9227-36.994117.9893
50.28362.1481-1.18513.347-0.78531.0266-0.0265-0.2007-0.13040.29820.10790.16960.2763-0.0839-0.0813-0.0454-0.02970.02710.12610.1231-0.04-25.1405-31.109936.1027
60.5465-0.12330.05480.22850.01791.04780.0046-0.1419-0.04540.020.03220.0118-0.0407-0.0071-0.0368-0.0527-0.01850.0062-0.00380.0077-0.0112-20.7292-20.265817.9407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|26 - 187}
2X-RAY DIFFRACTION2{A|188 - 194}
3X-RAY DIFFRACTION3{A|195 - 300}
4X-RAY DIFFRACTION4{A|301 - 311}
5X-RAY DIFFRACTION5{A|312 - 327}
6X-RAY DIFFRACTION6{A|328 - 389}

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