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- PDB-6nki: Structure of PhqB Reductase Domain from Penicillium fellutanum -

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Basic information

Entry
Database: PDB / ID: 6nki
TitleStructure of PhqB Reductase Domain from Penicillium fellutanum
ComponentsNRPS
KeywordsOXIDOREDUCTASE / Reductase
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases) / amino acid activation for nonribosomal peptide biosynthetic process / alkaloid metabolic process / secondary metabolite biosynthetic process / Oxidoreductases / ligase activity / phosphopantetheine binding / isomerase activity / oxidoreductase activity / cytoplasm
Similarity search - Function
Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / ANL, N-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / ANL, N-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / Nonribisomal peptide synthase phqB
Similarity search - Component
Biological speciesPenicillium fellutanum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDan, Q. / Newmister, S.A. / 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

Downloads & links

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Assembly

Deposited unit
A: NRPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0912
Polymers47,3461
Non-polymers7451
Water00
1
A: NRPS
hetero molecules

A: NRPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1824
Polymers94,6912
Non-polymers1,4912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area4420 Å2
ΔGint-17 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.636, 91.644, 124.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein NRPS


Mass: 47345.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence is unknown for twenty residues at the N-terminus of the PhqB reductase domain crystal structure due to disconnectivity and poor quality of local electron density, which led to a ploy-ALA build.
Source: (gene. exp.) Penicillium fellutanum (fungus) / Gene: phqB / Production host: Escherichia coli (E. coli) / References: UniProt: L0E2U2
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: 10% PEG 8000, 200 mM MgCl2, 100 mM Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→45.82 Å / Num. obs: 14760 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 79.11 Å2 / CC1/2: 1 / Rrim(I) all: 0.077 / Net I/σ(I): 20.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1433 / CC1/2: 0.64 / Rrim(I) all: 2.57 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.82 Å / SU ML: 0.5102 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 40.2151
RfactorNum. reflection% reflection
Rfree0.3245 1476 10.01 %
Rwork0.2653 --
obs0.2706 14746 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 127.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 48 0 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962845
X-RAY DIFFRACTIONf_angle_d1.24883915
X-RAY DIFFRACTIONf_chiral_restr0.0711449
X-RAY DIFFRACTIONf_plane_restr0.008487
X-RAY DIFFRACTIONf_dihedral_angle_d16.7598977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.3891300.40411177X-RAY DIFFRACTION99.85
2.68-2.780.44181330.42321196X-RAY DIFFRACTION99.92
2.78-2.890.46931320.36071177X-RAY DIFFRACTION99.85
2.89-3.020.43291320.33781203X-RAY DIFFRACTION99.55
3.02-3.180.37791310.31661173X-RAY DIFFRACTION99.92
3.18-3.380.38591340.32261199X-RAY DIFFRACTION99.85
3.38-3.640.39851350.29781218X-RAY DIFFRACTION100
3.64-4.010.28851320.25091193X-RAY DIFFRACTION100
4.01-4.580.26091360.21231225X-RAY DIFFRACTION100
4.58-5.770.26841360.23311222X-RAY DIFFRACTION99.85
5.77-45.830.3281450.25231287X-RAY DIFFRACTION99.58

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