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- PDB-6kbc: Crystal structure of CghA with Sch210972 -

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Basic information

Entry
Database: PDB / ID: 6kbc
TitleCrystal structure of CghA with Sch210972
ComponentsCghA
KeywordsUNKNOWN FUNCTION / Diels-alderase
Function / homologyIsomerases; Intramolecular lyases / isomerase activity / Chem-WK1 / Diels-Alderase cghA
Function and homology information
Biological speciesChaetomium globosum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHara, K. / Hashimoto, H. / Maeda, N. / 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 2.0Aug 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_mon_prot_cis / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _entity.pdbx_number_of_molecules ..._cell.volume / _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site.pdbx_num_residues / _symmetry.space_group_name_Hall
Description: Model completeness
Details: To respond to the following reviewer's comment. The pdb files submitted for review include protons, which presumably are not observed in the X-ray density at this resolution. Protons do not ...Details: To respond to the following reviewer's comment. The pdb files submitted for review include protons, which presumably are not observed in the X-ray density at this resolution. Protons do not appear to be added correctly in many places. Please ensure these are not included in the files submitted to the PDB. Likely due to the presence of a proton in refinement, the C-O distances in the carboxylate group differ (1.224 vs. 1.312 Ang). It seems unlikely that the underlying data justifies such a difference. The carboxylate group is almost certainly not protonated, which should lead to almost equal C-O distances. (Due to the environment, the pKa of this carboxylate should be significantly lower than that in solution.) Please refine these coordinates (e.g. use unprotonated carboxylate in refinement).
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 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 2.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: CghA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6112
Polymers44,1651
Non-polymers4461
Water5,747319
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 area15470 Å2
Unit cell
Length a, b, c (Å)75.247, 75.247, 189.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-620-

HOH

21A-815-

HOH

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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: Chemical ChemComp-WK1 / (2S)-3-[(2S,4E)-4-[[(1R,2S,4aR,6S,8R,8aS)-2-[(E)-but-2-en-2-yl]-6,8-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-oxidanyl-methylidene]-3,5-bis(oxidanylidene)pyrrolidin-2-yl]-2-methyl-2-oxidanyl-propanoic acid


Mass: 445.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.04 Å3/Da / Density % sol: 59.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, MES pH 6.5

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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 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. obs: 38280 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 27.31 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.99
Reflection shellResolution: 1.99→2.1 Å / Rmerge(I) obs: 0.281 / Num. unique obs: 5979

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KAW

6kaw


Resolution: 1.99→19.82 Å / SU ML: 0.1568 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1849 4.83 %
Rwork0.1838 36410 -
obs0.185 38259 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.28 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 32 319 3251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083015
X-RAY DIFFRACTIONf_angle_d1.23244114
X-RAY DIFFRACTIONf_chiral_restr0.0683440
X-RAY DIFFRACTIONf_plane_restr0.0071534
X-RAY DIFFRACTIONf_dihedral_angle_d17.49751065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.25781400.21082707X-RAY DIFFRACTION98
2.04-2.10.22691430.1962729X-RAY DIFFRACTION99.9
2.1-2.170.23061290.19622760X-RAY DIFFRACTION99.86
2.17-2.250.23881600.20092722X-RAY DIFFRACTION99.93
2.25-2.340.25211290.2012786X-RAY DIFFRACTION100
2.34-2.440.21571460.20082759X-RAY DIFFRACTION99.9
2.44-2.570.19731270.18952781X-RAY DIFFRACTION100
2.57-2.730.19811520.19572777X-RAY DIFFRACTION99.97
2.73-2.940.24541430.20612802X-RAY DIFFRACTION99.93
2.94-3.240.21081200.19232852X-RAY DIFFRACTION100
3.24-3.70.21231640.18262799X-RAY DIFFRACTION100
3.7-4.660.17721300.15342903X-RAY DIFFRACTION99.97
4.66-19.820.18861660.17443033X-RAY DIFFRACTION100

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