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- PDB-7kpt: Crystal structure of CtdE in complex with FAD and substrate 4 -

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Basic information

Entry
Database: PDB / ID: 7kpt
TitleCrystal structure of CtdE in complex with FAD and substrate 4
ComponentsFAD-dependent monooxygenase CtdE
KeywordsBIOSYNTHETIC PROTEIN / FAD monooxygenase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / Chem-WU4
Function and homology information
Biological speciesPenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsZhao, B. / Hu, L.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins.
Authors: Liu, Z. / Zhao, F. / Zhao, B. / Yang, J. / Ferrara, J. / Sankaran, B. / Venkataram Prasad, B.V. / Kundu, B.B. / Phillips Jr., G.N. / Gao, Y. / Hu, L. / Zhu, T. / Gao, X.
History
DepositionNov 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: FAD-dependent monooxygenase CtdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1015
Polymers49,7861
Non-polymers1,3154
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.279, 48.527, 67.643
Angle α, β, γ (deg.)90.000, 114.488, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD-dependent monooxygenase CtdE


Mass: 49786.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium citrinum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-WU4 / (6aR,7aS,11S,13aS)-6,6,11-trimethyl-4-(3-methylbut-2-en-1-yl)-6,6a,7,8,9,10,11,14-octahydro-5H,13H-13a,7a-(epiminomethano)quinolizino[2,3-b]carbazol-16-one


Mass: 431.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Calcium chloride, 20% w/v PEG 6000, 10% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2020
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 35699 / % possible obs: 98.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.04 / Rrim(I) all: 0.088 / Net I/σ(I): 26.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 6 / Num. unique obs: 1774 / CC1/2: 0.811 / Rpim(I) all: 0.421 / Rrim(I) all: 0.949 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KPQ

7kpq


Resolution: 1.91→34.02 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3811
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 1766 5.08 %
Rwork0.1696 32996 -
obs0.1713 34762 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.04 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 90 353 3654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823373
X-RAY DIFFRACTIONf_angle_d1.00024586
X-RAY DIFFRACTIONf_chiral_restr0.0647502
X-RAY DIFFRACTIONf_plane_restr0.0092597
X-RAY DIFFRACTIONf_dihedral_angle_d10.8383480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.23761020.19511951X-RAY DIFFRACTION73.4
1.96-2.020.22481290.18082247X-RAY DIFFRACTION85.96
2.02-2.080.24831430.18252469X-RAY DIFFRACTION94.78
2.08-2.160.22221350.17732593X-RAY DIFFRACTION98.27
2.16-2.250.2191310.17562625X-RAY DIFFRACTION98.71
2.25-2.350.23411410.18412595X-RAY DIFFRACTION98.88
2.35-2.470.21291080.17852642X-RAY DIFFRACTION99.06
2.47-2.630.2161310.17912651X-RAY DIFFRACTION99.18
2.63-2.830.21171440.1782636X-RAY DIFFRACTION99.29
2.83-3.110.21121420.17732629X-RAY DIFFRACTION99.5
3.11-3.560.20121610.1652637X-RAY DIFFRACTION99.54
3.56-4.490.16861510.14072677X-RAY DIFFRACTION99.79
4.49-34.020.17391480.1692644X-RAY DIFFRACTION96.14

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