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- PDB-7uf8: Structure of CtdP in complex with penicimutamide E and NADP+ -

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Basic information

Entry
Database: PDB / ID: 7uf8
TitleStructure of CtdP in complex with penicimutamide E and NADP+
ComponentsCtdP
KeywordsOXIDOREDUCTASE / Diels-Alderase / oxidioreductase / NmrA-like
Function / homologyPenicimutamide E / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesPenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRivera, S. / Liu, Z. / Newmister, S.A. / Gao, X. / Sherman, D.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 GM 132046-2 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35 GM118101 United States
CitationJournal: Nat.Chem. / Year: 2023
Title: An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity.
Authors: Liu, Z. / Rivera, S. / Newmister, S.A. / Sanders, J.N. / Nie, Q. / Liu, S. / Zhao, F. / Ferrara, J.D. / Shih, H.W. / Patil, S. / Xu, W. / Miller, M.D. / Phillips, G.N. / Houk, K.N. / Sherman, D.H. / Gao, X.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CtdP
B: CtdP
C: CtdP
D: CtdP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,16013
Polymers156,0564
Non-polymers4,1049
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.759, 166.759, 195.382
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein
CtdP


Mass: 39013.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium citrinum (fungus) / Gene: ctdP / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-N3L / Penicimutamide E


Mass: 335.443 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H25N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: 0.1 M BisTris pH 6.75, 25% PEG monomethyl ether 2000, 0.1 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→48.36 Å / Num. obs: 55814 / % possible obs: 99.8 % / Redundancy: 21.13 % / Biso Wilson estimate: 60.06 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.174 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 2.79 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 16814 / CC1/2: 0.826 / Rrim(I) all: 2.85 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDS20210322data reduction
PHENIX1.19.2_4158refinement
Coot0.9.5model building
PHASER1.19.2_4158phasing
PDB_EXTRACTdata extraction
XDSdata processing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→48.36 Å / SU ML: 0.3985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 1996 3.58 %
Rwork0.2238 53737 -
obs0.2251 55733 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10373 0 281 115 10769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016210953
X-RAY DIFFRACTIONf_angle_d1.939414925
X-RAY DIFFRACTIONf_chiral_restr0.06061564
X-RAY DIFFRACTIONf_plane_restr0.01211914
X-RAY DIFFRACTIONf_dihedral_angle_d17.63573892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.38771370.33173680X-RAY DIFFRACTION97.1
2.56-2.630.40011380.32233757X-RAY DIFFRACTION99.67
2.63-2.710.40671410.32883783X-RAY DIFFRACTION99.77
2.71-2.80.37791410.32833788X-RAY DIFFRACTION99.7
2.8-2.890.35591390.29013766X-RAY DIFFRACTION99.72
2.89-3.010.33171420.2743813X-RAY DIFFRACTION99.57
3.01-3.150.3091420.28723806X-RAY DIFFRACTION99.8
3.15-3.310.34271410.28743792X-RAY DIFFRACTION99.8
3.31-3.520.33161430.25633837X-RAY DIFFRACTION99.95
3.52-3.790.29381440.2223854X-RAY DIFFRACTION99.97
3.79-4.170.27191430.19843860X-RAY DIFFRACTION99.98
4.17-4.780.19331440.17513897X-RAY DIFFRACTION100
4.78-6.020.17971480.18693948X-RAY DIFFRACTION100
6.02-48.360.19871530.19044156X-RAY DIFFRACTION99.88

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