[English] 日本語
Yorodumi
- PDB-1tkw: The transient complex of poplar plastocyanin with turnip cytochro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tkw
TitleThe transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR
Components
  • Cytochrome f
  • Plastocyanin A
KeywordsPHOTOSYNTHESIS / Electron transfer / paramagnetic / rigid body calculations
Function / homology
Function and homology information


electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / iron ion binding / copper ion binding / heme binding
Similarity search - Function
Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type ...Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Rudiment single hybrid motif / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Cupredoxins - blue copper proteins / Cupredoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Plastocyanin A, chloroplastic / Cytochrome f
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
Brassica rapa subsp. rapa (turnip)
MethodSOLUTION NMR / Rigid body docking using intermolecular pseudocontact shifts restraints, chemical shift perturbation restraints, electrostatic restraints.
AuthorsLange, C. / Cornvik, T. / Diaz-Moreno, I. / Ubbink, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2005
Title: The transient complex of poplar plastocyanin with cytochrome f: effects of ionic strength and pH
Authors: Lange, C. / Cornvik, T. / Diaz-Moreno, I. / Ubbink, M.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Plastocyanin A
B: Cytochrome f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7214
Polymers38,0392
Non-polymers6822
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 104structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein Plastocyanin A


Mass: 10493.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus nigra (black poplar) / Gene: PETE / Plasmid: pETPC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00299
#2: Protein Cytochrome f


Mass: 27545.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa subsp. rapa (turnip) / Species: Brassica rapa / Strain: subsp. rapa / Gene: PETA / Plasmid: pTC1 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P36438
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N HSQC
2222D 15N HSQC
NMR detailsText: This structure was determined using the XRD structures of plastocyanin and cytochrome f, docked on the basis of intermolecular pseudocontact shifts and chemical shift perturbations due to binding.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.094% H2O, 6% D2O
20.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate94% H2O, 6% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 61 atm303 K
211 mM 61 atm303 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Azara2.7W. Boucherprocessing
ANSIGAnsig-for-Windows 1.02P. Kraulis, M. Helgstranddata analysis
X-PLORXPLOR-NIH 2.9.1structure solution
X-PLORXPLOR-NIH 2.9.1refinement
RefinementMethod: Rigid body docking using intermolecular pseudocontact shifts restraints, chemical shift perturbation restraints, electrostatic restraints.
Software ordinal: 1
Details: The structures are based on 38 chemical shift perturbation restraints, 42 pseudocontact shifts restraints, 42 pseudocontact angle restraints, 120 minimal distance restraints and 4 ...Details: The structures are based on 38 chemical shift perturbation restraints, 42 pseudocontact shifts restraints, 42 pseudocontact angle restraints, 120 minimal distance restraints and 4 electrostatic restraints. Backbone RMSD (in Angstrom) with the mean for each model: 1: 1.28, 2: 2.26, 3: 1.29, 4: 3.12, 5: 1.52, 6: 1.49, 7: 3.68, 8: 2.68, 9: 1.58, 10: 3.43, average=2.23+/-0.88
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 104 / Conformers submitted total number: 10

+
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