[English] 日本語
Yorodumi
- PDB-4lji: Crystal structure at 1.5 angstrom resolution of the PsbV2 cytochr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lji
TitleCrystal structure at 1.5 angstrom resolution of the PsbV2 cytochrome from the cyanobacterium thermosynechococcus elongatus
ComponentsCytochrome c-550-like protein
KeywordsELECTRON TRANSPORT / cytochrome c
Function / homology
Function and homology information


thylakoid membrane / photosystem II / photosynthesis / respiratory electron transport chain / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Photosystem II PsbV2, cytochrome / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-550-like protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.508 Å
AuthorsSuga, M. / Lai, T.-L. / Sugiura, M. / Shen, J.-R. / Boussac, A.
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structure at 1.5 angstrom resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus
Authors: Suga, M. / Lai, T.-L. / Sugiura, M. / Shen, J.-R. / Boussac, A.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 16, 2013Group: Database references
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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.label_atom_id / _atom_site.label_comp_id / _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.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c-550-like protein
B: Cytochrome c-550-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9795
Polymers30,7062
Non-polymers1,2723
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-68 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.421, 38.430, 47.779
Angle α, β, γ (deg.)71.86, 82.22, 69.38
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Cytochrome c-550-like protein


Mass: 15353.153 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Genus: psbV2 / Strain: BP-1 / References: UniProt: Q8DJE2
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.78 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 72721 / Biso Wilson estimate: 17.68 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ARC

3arc
PDB Unreleased entry


Resolution: 1.508→45.385 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.19 / σ(F): 1.97 / Phase error: 28.32 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.251 3653 5.03 %
Rwork0.2163 --
obs0.2181 72652 94.76 %
all-76475 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.75 Å2 / Biso mean: 25.6731 Å2 / Biso min: 9.84 Å2
Refinement stepCycle: LAST / Resolution: 1.508→45.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 87 121 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112202
X-RAY DIFFRACTIONf_angle_d1.4153026
X-RAY DIFFRACTIONf_chiral_restr0.101338
X-RAY DIFFRACTIONf_plane_restr0.008384
X-RAY DIFFRACTIONf_dihedral_angle_d13.455822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5077-1.52760.33971050.28292046215174
1.5276-1.54850.25141430.26462666280992
1.5485-1.57060.28331270.25792519264692
1.5706-1.5940.27411200.24572663278392
1.594-1.6190.27321230.25212620274393
1.619-1.64550.32941490.25312575272494
1.6455-1.67390.28241330.25472655278894
1.6739-1.70430.31151410.24532654279594
1.7043-1.73710.25451190.24522631275094
1.7371-1.77260.28861610.24192612277394
1.7726-1.81110.3291400.2372748288898
1.8111-1.85320.32421280.23352743287199
1.8532-1.89960.26351610.23672840300199
1.8996-1.95090.27231320.23482673280599
1.9509-2.00830.26461310.22982820295198
2.0083-2.07320.26981670.22062714288198
2.0732-2.14730.2941360.22522729286597
2.1473-2.23320.2481290.21452712284197
2.2332-2.33490.25041390.22042721286096
2.3349-2.4580.2861550.22362670282596
2.458-2.61190.24381480.22022712286096
2.6119-2.81360.3231480.22212706285497
2.8136-3.09670.25561800.21662645282597
3.0967-3.54460.23641280.21692700282896
3.5446-4.46520.19141530.17832587274093
4.4652-45.40590.20061570.18662638279594
Refinement TLS params.Method: refined / Origin x: -1.0045 Å / Origin y: -0.4565 Å / Origin z: 0.078 Å
111213212223313233
T0.1138 Å20.0101 Å2-0.0225 Å2-0.1172 Å20.0301 Å2--0.1234 Å2
L0.6825 °20.1188 °2-0.4319 °2-1.1149 °20.9227 °2--1.8456 °2
S0.0324 Å °-0.0286 Å °-0.0073 Å °-0.0002 Å °0.0601 Å °-0.0275 Å °0.0055 Å °0.0289 Å °-0.087 Å °
Refinement TLS groupSelection details: ALL

+
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://pdbjlvh1.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