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- PDB-7kpq: Crystal structure of CtdE in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 7kpq
TitleCrystal structure of CtdE in complex with FAD
ComponentsFAD-dependent monooxygenase CtdE
KeywordsBIOSYNTHETIC PROTEIN / FAD monooxygenase
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesPenicillium citrinum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)50,5722
Polymers49,7861
Non-polymers7861
Water5,044280
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)88.998, 88.998, 108.516
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-777-

HOH

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Components

#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)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M calcium chloride dihydrate, 20% w/v PEG6000, 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: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2020
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.1→34.41 Å / Num. obs: 29584 / % possible obs: 99.64 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.82 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Net I/σ(I): 32.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1468 / CC1/2: 0.762 / Rpim(I) all: 0.348 / % possible all: 98.83

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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: 6PVH

6pvh


Resolution: 2.1→34.41 Å / SU ML: 0.1713 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3078
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 1427 4.82 %
Rwork0.1856 28157 -
obs0.1873 29584 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 53 280 3307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393091
X-RAY DIFFRACTIONf_angle_d0.79564194
X-RAY DIFFRACTIONf_chiral_restr0.057462
X-RAY DIFFRACTIONf_plane_restr0.0052533
X-RAY DIFFRACTIONf_dihedral_angle_d10.9273415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.26291380.23542723X-RAY DIFFRACTION97.48
2.17-2.260.34241460.30752722X-RAY DIFFRACTION98.69
2.26-2.360.28281130.22982806X-RAY DIFFRACTION99.45
2.36-2.480.2321440.1932810X-RAY DIFFRACTION100
2.48-2.640.24541450.19662793X-RAY DIFFRACTION100
2.64-2.840.26911460.1932801X-RAY DIFFRACTION100
2.84-3.130.24711550.18642811X-RAY DIFFRACTION100
3.13-3.580.21081450.16522832X-RAY DIFFRACTION100
3.58-4.510.17261550.1512865X-RAY DIFFRACTION99.97
4.51-34.410.17931400.16842994X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.69893580659-0.48938819527-0.2086380234832.6858235176-0.2974128221151.9647351868-0.156377267659-0.0617621171671-0.478683140403-0.0269065351482-0.02771635680790.1472696300180.532522660783-0.1588323513650.07330332578620.290518007230.06774388305370.07826167675980.0888769167877-0.007425644848630.24353695584523.87710976756.34444856828-6.47939141953
21.94745650771-0.705023001806-0.7005926238372.32528107989-0.2156084873571.38450825912-0.1188727502190.0738272063191-0.256767381083-0.155422501771-0.016215751233-0.09914350298590.2098987241940.139721293725-0.02382726184590.3000038564550.1562257321790.05721553119480.1490365799610.002136295839340.13996553242834.512819446814.6230522094-15.8671495289
31.071252694770.803331028093-0.654222204041.151619201590.333868284621.736368340890.0259901656154-0.0110254705001-0.131959656712-0.039895582344-0.00777556462522-0.06593743291630.05053318119930.00732093102186-0.08492327550610.2613796306990.1115757146960.02577753401220.1080304304560.02560651619970.14401344191334.818275082118.7021044476-9.15202790832
42.330047817990.5862712941170.864973570310.880862679180.4597365661791.472437991260.00410249283173-0.259178759115-0.1747791937020.05313736903370.0590753926791-0.1906441955440.04330477397230.249971706694-0.03439849972370.1481691689930.06624375763850.009099847049080.2337677326440.02769770214440.16130846659244.271319163919.53300149465.00342498848
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 323 through 431 )323 - 431296 - 383
22chain 'A' and (resid 19 through 86 )19 - 861 - 68
33chain 'A' and (resid 87 through 178 )87 - 17869 - 151
44chain 'A' and (resid 179 through 322 )179 - 322152 - 295

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