[English] 日本語
Yorodumi
- PDB-5aui: Crystal structure of Ferredoxin from Thermosynechococcus elongatus -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


electron transport chain / 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. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding 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. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more