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- PDB-6nkk: Structure of PhqE Reductase/Diels-Alderase from Penicillium fellu... -

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Basic information

Entry
Database: PDB / ID: 6nkk
TitleStructure of PhqE Reductase/Diels-Alderase from Penicillium fellutanum in complex with NADP+ and premalbrancheamide
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
: / 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-PM7 / Short-chain dehydrogenase/reductase phqE
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)171,80118
Polymers165,3286
Non-polymers6,47312
Water1,964109
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)114,53412
Polymers110,2184
Non-polymers4,3158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17430 Å2
ΔGint-112 kcal/mol
Surface area35130 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)114,53412
Polymers110,2184
Non-polymers4,3158
Water362
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 area15180 Å2
ΔGint-83 kcal/mol
Surface area37960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.586, 117.248, 64.809
Angle α, β, γ (deg.)90.000, 107.960, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA9 - 2659 - 265
2THRTHRchain BBB9 - 2659 - 265
3ASPASPchain CCC10 - 26510 - 265
4THRTHRchain DDD9 - 2659 - 265
5ASPASPchain EEE10 - 26510 - 265
6ASPASPchain FFF10 - 26510 - 265

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Components

#1: Protein
Short chain dehydrogenase


Mass: 27554.613 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-PM7 / (5aS,12aS,13aS)-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7,6-b]carbazol-14-one / premalbrancheamide E


Mass: 335.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H25N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 19% PEG 3350, 150 mM DL-malic acid, 2.5% ethylene glycol, 1 mM premalbrancheamide, 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: Feb 7, 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: 2.29→46.38 Å / Num. obs: 65748 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 8.7
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→46.377 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 42.23
RfactorNum. reflection% reflection
Rfree0.3357 3153 4.8 %
Rwork0.2932 --
obs0.2953 65742 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.93 Å2 / Biso mean: 75.1361 Å2 / Biso min: 23.92 Å2
Refinement stepCycle: final / Resolution: 2.299→46.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11175 0 438 109 11722
Biso mean--68.58 48.36 -
Num. residues----1539
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4824X-RAY DIFFRACTION6.973TORSIONAL
12B4824X-RAY DIFFRACTION6.973TORSIONAL
13C4824X-RAY DIFFRACTION6.973TORSIONAL
14D4824X-RAY DIFFRACTION6.973TORSIONAL
15E4824X-RAY DIFFRACTION6.973TORSIONAL
16F4824X-RAY DIFFRACTION6.973TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2994-2.33370.47791300.40922585271595
2.3337-2.37020.40051620.38162636279899
2.3702-2.40910.40761220.38112785290799
2.4091-2.45060.42331180.3722713283199
2.4506-2.49520.42281820.37612709289199
2.4952-2.54310.38741620.34912592275499
2.5431-2.59510.46621340.3442773290799
2.5951-2.65150.3991520.33922668282099
2.6515-2.71310.42811240.34652728285299
2.7131-2.7810.444990.33862753285299
2.781-2.85620.39371510.34482730288199
2.8562-2.94020.42591300.36212707283799
2.9402-3.03510.39231250.343227172842100
3.0351-3.14350.37231260.334827512877100
3.1435-3.26940.48511430.340427362879100
3.2694-3.41810.38081160.32227642880100
3.4181-3.59830.28931400.292527312871100
3.5983-3.82360.33431570.28132683284099
3.8236-4.11870.30511220.276427622884100
4.1187-4.53280.25181240.246227602884100
4.5328-5.1880.2831480.240527552903100
5.188-6.53340.31531630.27527412904100
6.5334-46.38620.23381230.20862810293399
Refinement TLS params.Method: refined / Origin x: 16.7116 Å / Origin y: 40.0556 Å / Origin z: 34.7385 Å
111213212223313233
T0.0762 Å20.176 Å20.2314 Å2-0.3897 Å2-0.2174 Å2--0.241 Å2
L0.7386 °20.1241 °20.7462 °2-1.1313 °2-0.1769 °2--1.5814 °2
S0.1001 Å °0.1982 Å °-0.0337 Å °0.0252 Å °-0.0635 Å °-0.0011 Å °-0.0737 Å °0.2818 Å °0.0022 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 - 901
5X-RAY DIFFRACTION1allC10 - 265
6X-RAY DIFFRACTION1allC801 - 901
7X-RAY DIFFRACTION1allD9 - 265
8X-RAY DIFFRACTION1allD801 - 901
9X-RAY DIFFRACTION1allE10 - 265
10X-RAY DIFFRACTION1allE801 - 901
11X-RAY DIFFRACTION1allF10 - 265
12X-RAY DIFFRACTION1allF801 - 901
13X-RAY DIFFRACTION1allG1 - 109

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