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- PDB-6nkm: Structure of PhqE D166N Reductase/Diels-Alderase from Penicillium... -

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Basic information

Entry
Database: PDB / ID: 6nkm
TitleStructure of PhqE D166N Reductase/Diels-Alderase from Penicillium fellutanum in complex with NADP+ and substrate
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / Reductase / Diels-Alderase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors / alkaloid metabolic process / oxidoreductase activity / membrane
Similarity search - Function
SDR-like rossmann domain / : / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-ZWP / Short-chain dehydrogenase/reductase phqE
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.896 Å
AuthorsNewmister, S.A. / Dan, Q. / Smith, J.L. / Sherman, D.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA070375 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118101 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK042303 United States
CitationJournal: Nat.Chem. / Year: 2019
Title: Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase.
Authors: Dan, Q. / Newmister, S.A. / Klas, K.R. / Fraley, A.E. / McAfoos, T.J. / Somoza, A.D. / Sunderhaus, J.D. / Ye, Y. / Shende, V.V. / Yu, F. / Sanders, J.N. / Brown, W.C. / Zhao, L. / Paton, R.S. ...Authors: Dan, Q. / Newmister, S.A. / Klas, K.R. / Fraley, A.E. / McAfoos, T.J. / Somoza, A.D. / Sunderhaus, J.D. / Ye, Y. / Shende, V.V. / Yu, F. / Sanders, J.N. / Brown, W.C. / Zhao, L. / Paton, R.S. / Houk, K.N. / Smith, J.L. / Sherman, D.H. / Williams, R.M.
History
DepositionJan 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
D: Short chain dehydrogenase
E: Short chain dehydrogenase
F: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,11413
Polymers165,3226
Non-polymers4,7927
Water3,531196
1
A: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
D: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5209
Polymers110,2154
Non-polymers3,3055
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17560 Å2
ΔGint-118 kcal/mol
Surface area35500 Å2
MethodPISA
2
E: Short chain dehydrogenase
hetero molecules

E: Short chain dehydrogenase
hetero molecules

F: Short chain dehydrogenase
hetero molecules

F: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1888
Polymers110,2154
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_546-x,y-1,-z+11
Buried area14580 Å2
ΔGint-93 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.484, 117.194, 63.731
Angle α, β, γ (deg.)90.000, 107.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-953-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 9 through 265 or resid 801))
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 9 through 265 or resid 801))A0
211chain BB9 - 265
311chain CC9 - 265
411chain DD9 - 265
511chain EE9 - 265
611chain FF9 - 265

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Components

#1: Protein
Short chain dehydrogenase


Mass: 27553.627 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium fellutanum (fungus) / Gene: phqE / Production host: Escherichia coli (E. coli) / References: UniProt: L0E2Z4
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ZWP / 3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-8H-pyrrolo[1,2-a]pyrazin-5-ium-1-olate


Mass: 331.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.75
Details: 18% PEG 3350, 200 mM NaCl, 50 mM BisTris pH 6.75, 2.5% ethylene glycol, 1 mM ZWP, 4 mM NADP+, 1% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.89→48.76 Å / Num. obs: 112785 / % possible obs: 97.2 % / Redundancy: 6.9 % / Net I/σ(I): 12.8
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.7 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.896→48.758 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.43
RfactorNum. reflection% reflection
Rfree0.3062 5561 4.93 %
Rwork0.2739 --
obs0.2755 112779 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 234.81 Å2 / Biso mean: 68.3677 Å2 / Biso min: 27.35 Å2
Refinement stepCycle: final / Resolution: 1.896→48.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11192 0 313 196 11701
Biso mean--61.17 50.79 -
Num. residues----1542
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4788X-RAY DIFFRACTION7.575TORSIONAL
12B4788X-RAY DIFFRACTION7.575TORSIONAL
13C4788X-RAY DIFFRACTION7.575TORSIONAL
14D4788X-RAY DIFFRACTION7.575TORSIONAL
15E4788X-RAY DIFFRACTION7.575TORSIONAL
16F4788X-RAY DIFFRACTION7.575TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8959-1.91740.52111640.51083198336288
1.9174-1.940.46341460.46723437358392
1.94-1.96360.45011500.44293442359293
1.9636-1.98850.46841870.42773495368295
1.9885-2.01470.50221830.38883500368396
2.0147-2.04230.41482180.38793521373997
2.0423-2.07140.40272090.3843556376597
2.0714-2.10240.40781950.35033492368797
2.1024-2.13520.37391820.32133602378497
2.1352-2.17020.33541900.32243514370497
2.1702-2.20760.32821840.32013604378897
2.2076-2.24780.38371780.31543563374197
2.2478-2.2910.32611810.31313582376398
2.291-2.33780.34261790.29523604378398
2.3378-2.38860.36521880.30623574376298
2.3886-2.44420.31721710.31313610378198
2.4442-2.50530.35531940.31673591378598
2.5053-2.5730.37611590.30513607376698
2.573-2.64870.34241880.31033606379498
2.6487-2.73420.36151940.31763637383198
2.7342-2.83190.37161970.31173578377598
2.8319-2.94530.32072010.3173612381398
2.9453-3.07930.33481710.30133655382698
3.0793-3.24170.35452270.30293584381199
3.2417-3.44470.31871950.28183637383299
3.4447-3.71060.29221920.25793634382699
3.7106-4.08380.27771860.24593656384299
4.0838-4.67440.24571780.21773693387199
4.6744-5.88760.23561740.24013707388199
5.8876-48.77410.24742000.21723727392799
Refinement TLS params.Method: refined / Origin x: 17.2139 Å / Origin y: 40.1272 Å / Origin z: 34.2437 Å
111213212223313233
T0.2852 Å20.1153 Å20.0679 Å2-0.3673 Å2-0.1125 Å2--0.2816 Å2
L0.8115 °2-0.0612 °20.5316 °2-0.6421 °2-0.1536 °2--0.8351 °2
S0.149 Å °0.1761 Å °-0.0124 Å °-0.0431 Å °-0.1092 Å °0.0442 Å °0.0426 Å °0.1807 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 265
2X-RAY DIFFRACTION1allA801 - 901
3X-RAY DIFFRACTION1allB9 - 265
4X-RAY DIFFRACTION1allB801
5X-RAY DIFFRACTION1allC9 - 265
6X-RAY DIFFRACTION1allC801
7X-RAY DIFFRACTION1allD9 - 265
8X-RAY DIFFRACTION1allD801
9X-RAY DIFFRACTION1allE9 - 265
10X-RAY DIFFRACTION1allE801
11X-RAY DIFFRACTION1allF9 - 265
12X-RAY DIFFRACTION1allF801
13X-RAY DIFFRACTION1allG1 - 196

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