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- PDB-5aui: Crystal structure of Ferredoxin from Thermosynechococcus elongatus -

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Entry
Database: PDB / ID: 5aui
TitleCrystal structure of Ferredoxin from Thermosynechococcus elongatus
ComponentsFerredoxin-1
KeywordsELECTRON TRANSPORT / Electron transfer protein
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / FE2/S2 (INORGANIC) CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsKurisu, G. / Shinmura, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)GS016 (Cabinet Office of Japan) Japan
CitationJournal: Biochemistry / Year: 2015
Title: X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin
Authors: Mutoh, R. / Muraki, N. / Shinmura, K. / Kubota-Kawai, H. / Lee, Y.H. / Nowaczyk, M.M. / Rogner, M. / Hase, T. / Ikegami, T. / Kurisu, G.
History
DepositionApr 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Feb 9, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / audit_author / cell / chem_comp / citation_author / diffrn / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_related_exp_data_set / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conn / struct_conn_type / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _audit_author.identifier_ORCID / _cell.angle_beta / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation_author.identifier_ORCID / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_contact_author.address_1 / _pdbx_contact_author.address_2 / _pdbx_contact_author.address_3 / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.value / _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 / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _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.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _reflns.d_resolution_high / _reflns_shell.d_res_high / _reflns_shell.number_unique_obs / _struct.pdbx_CASP_flag / _struct.title / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_label_comp_id
Description: Model completeness
Details: We found that our original assignment of the post-translation midification was wrong.
Provider: author / Type: Coordinate replacement
Revision 3.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0193
Polymers10,7231
Non-polymers2962
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-16 kcal/mol
Surface area5120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.441, 53.314, 32.278
Angle α, β, γ (deg.)90.000, 92.384, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ferredoxin-1 / / Ferredoxin I


Mass: 10722.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: It contains an expected post-translational modification revealed by this high-resolution X-ray analysis.
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Gene: petF1, petF, tsl1009 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A3C9
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.6 M Ammonium sulfate, 0.2% benzamidine hydrochloride, 3% (w/v) 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.499→50 Å / Num. obs: 15300 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 35.5
Reflection shellResolution: 1.499→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2193 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOLREPphasing
Coot0.9.6.1.1model building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B2G

3b2g


Resolution: 1.499→32.25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.145 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.183 751 4.967 %RANDOM
Rwork0.1589 14370 --
all0.16 ---
obs-15121 98.182 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.133 Å2-0 Å2-0.064 Å2
2---0.141 Å20 Å2
3---0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.499→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms749 0 13 42 804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013798
X-RAY DIFFRACTIONr_bond_other_d0.0180.016722
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.6571080
X-RAY DIFFRACTIONr_angle_other_deg1.5291.5911677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70725.36641
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.48101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59515135
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg28.314154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.565153
X-RAY DIFFRACTIONr_chiral_restr0.0970.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02160
X-RAY DIFFRACTIONr_nbd_refined0.2060.2126
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.2705
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2389
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.26
X-RAY DIFFRACTIONr_nbd_other0.1860.220
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.28
X-RAY DIFFRACTIONr_mcbond_it1.8981.96399
X-RAY DIFFRACTIONr_mcbond_other1.8241.95398
X-RAY DIFFRACTIONr_mcangle_it2.7772.928501
X-RAY DIFFRACTIONr_mcangle_other2.7922.936502
X-RAY DIFFRACTIONr_scbond_it3.6282.464399
X-RAY DIFFRACTIONr_scbond_other3.6242.468400
X-RAY DIFFRACTIONr_scangle_it5.5783.532576
X-RAY DIFFRACTIONr_scangle_other5.5743.533576
X-RAY DIFFRACTIONr_lrange_it6.09724.384816
X-RAY DIFFRACTIONr_lrange_other6.09124.356816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.5380.208500.204919X-RAY DIFFRACTION86.1333
1.538-1.580.242500.1811011X-RAY DIFFRACTION96.8066
1.58-1.6260.207590.1681016X-RAY DIFFRACTION98.8051
1.626-1.6760.185490.16970X-RAY DIFFRACTION98.8361
1.676-1.7310.155470.156959X-RAY DIFFRACTION99.211
1.731-1.7910.183540.148906X-RAY DIFFRACTION98.9691
1.791-1.8590.188490.143896X-RAY DIFFRACTION99.3691
1.859-1.9340.138380.143868X-RAY DIFFRACTION99.3421
1.934-2.020.16470.143821X-RAY DIFFRACTION99.5413
2.02-2.1180.185360.14787X-RAY DIFFRACTION99.5163
2.118-2.2320.13390.137757X-RAY DIFFRACTION99.6245
2.232-2.3670.219380.153710X-RAY DIFFRACTION99.7333
2.367-2.5290.178320.147672X-RAY DIFFRACTION100
2.529-2.7310.236370.161625X-RAY DIFFRACTION99.8492
2.731-2.9890.151400.163577X-RAY DIFFRACTION99.3559
2.989-3.3380.138240.176516X-RAY DIFFRACTION99.0826
3.338-3.8480.3170.157472X-RAY DIFFRACTION98.7879
3.848-4.6960.198210.146392X-RAY DIFFRACTION99.0408
4.696-6.5720.191150.188310X-RAY DIFFRACTION100
6.572-32.250.10690.197185X-RAY DIFFRACTION100

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