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- PDB-5u97: Crystal structure of Co-CAO1 in complex with piceatannol -

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Entry
Database: PDB / ID: 5u97
TitleCrystal structure of Co-CAO1 in complex with piceatannol
ComponentsCarotenoid oxygenase 1
KeywordsOXIDOREDUCTASE / carotenoid / cleavage / oxygenase / beta propeller / dioxygenase / piceatannol / carotenoid oxygenase
Function / homology
Function and homology information


carotenoid dioxygenase activity / carotene catabolic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / metal ion binding
Similarity search - Function
Carotenoid oxygenase / Retinal pigment epithelial membrane protein
Similarity search - Domain/homology
BENZOIC ACID / : / PICEATANNOL / Carotenoid cleavage oxygenase 1
Similarity search - Component
Biological speciesNeurospora crassa OR74A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSui, X. / Palczewski, K. / Banerjee, S. / Kiser, P.D.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY009339 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY020551 United States
Burroughs Wellcome Fund1015187 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA157735 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM77387 United States
Department of Veterans Affairs (VA, United States)BX002683 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structure and Spectroscopy of Alkene-Cleaving Dioxygenases Containing an Atypically Coordinated Non-Heme Iron Center.
Authors: Sui, X. / Weitz, A.C. / Farquhar, E.R. / Badiee, M. / Banerjee, S. / von Lintig, J. / Tochtrop, G.P. / Palczewski, K. / Hendrich, M.P. / Kiser, P.D.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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 / _citation_author.name / _struct_keywords.text
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.0Feb 8, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn / entity / entity_src_gen / exptl_crystal_grow / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_keywords / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal_grow.pdbx_details / _pdbx_audit_support.funding_organization / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_database_status.SG_entry / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_overall_ESU_R / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _reflns.pdbx_CC_half / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Ligand geometry
Details: Re-refinement using the CCP4 dictionary file for piceatannol
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carotenoid oxygenase 1
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,39325
Polymers237,9924
Non-polymers3,40121
Water30,6261700
1
A: Carotenoid oxygenase 1
D: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,90213
Polymers118,9962
Non-polymers1,90611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carotenoid oxygenase 1
C: Carotenoid oxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,49112
Polymers118,9962
Non-polymers1,49510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.050, 101.050, 448.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carotenoid oxygenase 1 /


Mass: 59497.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa OR74A (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: cao-1, NCU07008 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7S860

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Non-polymers , 5 types, 1721 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL / Piceatannol


Mass: 244.243 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C7H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1700 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: sodium polyacrylate, HEPES 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→47.86 Å / Num. obs: 220557 / % possible obs: 96.9 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 1.037 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 35436 / CC1/2: 0.411

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U8X

5u8x


Resolution: 1.85→47.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.951 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20584 9977 4.5 %RANDOM
Rwork0.18398 ---
obs0.18499 210580 96.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å2-0 Å2
2--0.22 Å20 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.85→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15949 0 232 1700 17881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01216942
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615255
X-RAY DIFFRACTIONr_angle_refined_deg1.11.65623066
X-RAY DIFFRACTIONr_angle_other_deg0.3821.57435178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37952037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.1199.375272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56810.692587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.69315119
X-RAY DIFFRACTIONr_chiral_restr0.0550.22311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024176
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6332.7168079
X-RAY DIFFRACTIONr_mcbond_other1.632.7168079
X-RAY DIFFRACTIONr_mcangle_it2.4394.87410133
X-RAY DIFFRACTIONr_mcangle_other2.444.87410134
X-RAY DIFFRACTIONr_scbond_it2.2973.0038863
X-RAY DIFFRACTIONr_scbond_other2.2963.0038864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7135.39512932
X-RAY DIFFRACTIONr_long_range_B_refined5.26231.8519166
X-RAY DIFFRACTIONr_long_range_B_other5.26231.8519167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 779 -
Rwork0.387 15158 -
obs--95.53 %

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