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- PDB-7avp: Crystal structure of marine actinobacteria clade rhodopsin (MAR) ... -

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Entry
Database: PDB / ID: 7avp
TitleCrystal structure of marine actinobacteria clade rhodopsin (MAR) in the O state
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / retinal / rhodopsin / bacteriorhodopsin / proton pump / ion transport / xanthorhodopsin
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / RETINAL / Bacteriorhodopsin
Function and homology information
Biological speciesCandidatus Actinomarina minuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsGushchin, I. / Polovinkin, V. / Kovalev, K. / Shevchenko, V. / Gordeliy, V.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0026 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)ANR-17-EURE-0003 France
CitationJournal: Sci Adv / Year: 2025
Title: Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.
Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / ...Authors: Bukhdruker, S. / Gushchin, I. / Shevchenko, V. / Kovalev, K. / Polovinkin, V. / Tsybrov, F. / Astashkin, R. / Alekseev, A. / Mikhaylov, A. / Bukhalovich, S. / Bratanov, D. / Ryzhykau, Y. / Kuklina, D. / Caramello, N. / Rokitskaya, T. / Antonenko, Y. / Rulev, M. / Stoev, C. / Zabelskii, D. / Round, E. / Rogachev, A. / Borshchevskiy, V. / Ghai, R. / Bourenkov, G. / Zeghouf, M. / Cherfils, J. / Engelhard, M. / Chizhov, I. / Rodriguez-Valera, F. / Bamberg, E. / Gordeliy, V.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Oct 2, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / cell / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conn / symmetry
Item: _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _cell.volume / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _struct_conn.pdbx_dist_value / _symmetry.space_group_name_Hall
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 3.0Apr 2, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _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_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct.title
Revision 3.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / struct_keywords
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,64720
Polymers24,2771
Non-polymers5,37019
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint85 kcal/mol
Surface area10050 Å2
Unit cell
Length a, b, c (Å)50.633, 40.417, 60.428
Angle α, β, γ (deg.)90.000, 101.370, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Components on special symmetry positions
IDModelComponents
11A-522-

HOH

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Components

#1: Protein Bacteriorhodopsin


Mass: 24277.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: S5DM51
#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C20H42
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H28O
Source: (gene. exp.) Candidatus Actinomarina minuta (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 10% PEG 6000 140 mM NaCl 0.1M NaAcetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.076→59.241 Å / Num. obs: 71975 / % possible obs: 89.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 10.28 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.024 / Net I/σ(I): 13.74
Reflection shellResolution: 1.076→1.181 Å / Mean I/σ(I) obs: 1.91 / Num. unique obs: 3599 / CC1/2: 0.7472 / Rpim(I) all: 0.364

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Processing

Software
NameVersionClassification
STARANISOdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
REFMAC5refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JSI

5jsi


Resolution: 1.09→59.24 Å / SU ML: 0.0625 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.3501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1526 3382 4.9 %RANDOM
Rwork0.1333 65654 --
obs0.1342 69036 69.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.14 Å2
Refinement stepCycle: LAST / Resolution: 1.09→59.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 179 200 2076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781989
X-RAY DIFFRACTIONf_angle_d0.98752651
X-RAY DIFFRACTIONf_chiral_restr0.0687280
X-RAY DIFFRACTIONf_plane_restr0.0085311
X-RAY DIFFRACTIONf_dihedral_angle_d17.2846793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.110.323240.449447X-RAY DIFFRACTION1.25
1.11-1.120.3407120.4172144X-RAY DIFFRACTION3.78
1.12-1.140.3741210.3557347X-RAY DIFFRACTION9.08
1.14-1.160.3165340.2755711X-RAY DIFFRACTION17.87
1.16-1.180.1991470.2141109X-RAY DIFFRACTION27.97
1.18-1.20.1953670.19581323X-RAY DIFFRACTION33.91
1.2-1.220.181840.19271577X-RAY DIFFRACTION40.4
1.22-1.250.2039940.18951950X-RAY DIFFRACTION49.49
1.25-1.280.23271300.19752467X-RAY DIFFRACTION62.77
1.28-1.310.18271580.19282950X-RAY DIFFRACTION75.09
1.31-1.340.19162120.1743352X-RAY DIFFRACTION86.13
1.34-1.380.16551690.17373645X-RAY DIFFRACTION92.28
1.38-1.420.18381750.16383753X-RAY DIFFRACTION94.81
1.42-1.460.18121760.15483767X-RAY DIFFRACTION95.96
1.46-1.510.15771850.13813704X-RAY DIFFRACTION92.97
1.51-1.570.14361990.12693815X-RAY DIFFRACTION97.21
1.57-1.650.12741900.10953841X-RAY DIFFRACTION97.34
1.65-1.730.12362150.10423854X-RAY DIFFRACTION97.41
1.73-1.840.14021960.10693796X-RAY DIFFRACTION96.45
1.84-1.980.12182100.10733774X-RAY DIFFRACTION95.95
1.98-2.180.12481940.10383927X-RAY DIFFRACTION98.56
2.18-2.50.12782070.10333938X-RAY DIFFRACTION98.95
2.5-3.150.12971910.11543878X-RAY DIFFRACTION96.58
3.15-59.240.18522120.16023985X-RAY DIFFRACTION97.33

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