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- PDB-6kaw: Crystal structure of CghA -

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Basic information

Entry
Database: PDB / ID: 6kaw
TitleCrystal structure of CghA
ComponentsCghA
KeywordsUNKNOWN FUNCTION / Diels-Alderase
Function / homologyIsomerases; Intramolecular lyases / isomerase activity / Diels-Alderase cghA
Function and homology information
Biological speciesChaetomium globosum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsHara, K. / Hashimoto, H. / Yokoyama, M. / Sato, M. / Watanabe, K.
CitationJournal: Nat Catal / Year: 2021
Title: Catalytic mechanism and endo-to-exo selectivity reversion of an octalin-forming natural Diels-Alderase
Authors: Sato, M. / Kishimoto, S. / Yokoyama, M. / Jamieson, C.S. / Narita, K. / Maeda, N. / Hara, K. / Hashimoto, H. / Tsunematsu, Y. / Houk, K.N. / Tang, Y. / Watanabe, K.
History
DepositionJun 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 27, 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

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Assembly

Deposited unit
A: CghA


Theoretical massNumber of molelcules
Total (without water)44,1651
Polymers44,1651
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16190 Å2
Unit cell
Length a, b, c (Å)76.016, 76.016, 190.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CghA


Mass: 44164.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) (fungus)
Strain: ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970
Gene: CHGG_02368 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2HBN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.11 Å3/Da / Density % sol: 60.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.01→20 Å / Num. obs: 38207 / % possible obs: 99.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 10.4
Reflection shellResolution: 2.01→2.13 Å / Rmerge(I) obs: 0.864 / Num. unique obs: 5995

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.01→20 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.66
RfactorNum. reflection% reflection
Rfree0.2184 1848 4.84 %
Rwork0.1903 --
obs0.1916 38184 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 0 417 3342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073007
X-RAY DIFFRACTIONf_angle_d1.0674098
X-RAY DIFFRACTIONf_dihedral_angle_d13.7161056
X-RAY DIFFRACTIONf_chiral_restr0.044440
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0066-2.06080.26221480.23812717X-RAY DIFFRACTION100
2.0608-2.12140.26461340.2242734X-RAY DIFFRACTION100
2.1214-2.18980.2311340.21852744X-RAY DIFFRACTION100
2.1898-2.26790.26851570.21142740X-RAY DIFFRACTION100
2.2679-2.35860.26581300.20872767X-RAY DIFFRACTION100
2.3586-2.46580.20161510.20772747X-RAY DIFFRACTION100
2.4658-2.59550.24461190.20372778X-RAY DIFFRACTION100
2.5955-2.75770.22181550.20662770X-RAY DIFFRACTION100
2.7577-2.970.24981430.20392801X-RAY DIFFRACTION100
2.97-3.26780.19251190.19712824X-RAY DIFFRACTION100
3.2678-3.73790.20561630.1782798X-RAY DIFFRACTION100
3.7379-4.69930.18551300.15562895X-RAY DIFFRACTION100
4.6993-20.00770.21081650.1783021X-RAY DIFFRACTION100

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