[English] 日本語
Yorodumi
- PDB-4i7z: Crystal structure of cytochrome b6f in DOPG, with disordered Ries... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i7z
TitleCrystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6
  • Cytochrome b6-f complex iron-sulfur subunit
KeywordsPHOTOSYNTHESIS / CYTOCHROME / MEMBRANE PROTEIN / PLASTOQUINOL:PLASTOCYANIN OXIDOREDUCTASE / PLASTOCYANIN / THYLAKOID MEMBRANE
Function / homology
Function and homology information


cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / quinol-cytochrome-c reductase activity / plasma membrane-derived thylakoid membrane / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / quinol-cytochrome-c reductase activity / plasma membrane-derived thylakoid membrane / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis / respiratory electron transport chain / monooxygenase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB ...Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Iron-sulfur subunit PetC transmembrane anchor / 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. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rudiment single hybrid motif / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-1E2 / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OZ2 / Cytochrome b6 ...Chem-1E2 / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OZ2 / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8
Similarity search - Component
Biological speciesMastigocladus laminosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.803 Å
AuthorsHasan, S.S. / Stofleth, J.T. / Yamashita, E. / Cramer, W.A.
CitationJournal: Biochemistry / Year: 2013
Title: Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis.
Authors: Hasan, S.S. / Stofleth, J.T. / Yamashita, E. / Cramer, W.A.
History
DepositionDec 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_ref_seq_dif.details / _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 b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,43127
Polymers107,6518
Non-polymers8,78019
Water23413
1
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules

A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,86254
Polymers215,30316
Non-polymers17,55938
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area75070 Å2
ΔGint-804 kcal/mol
Surface area68500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.451, 159.451, 362.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein , 3 types, 3 molecules ACD

#1: Protein Cytochrome b6


Mass: 24245.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791
#3: Protein Apocytochrome f


Mass: 31655.088 Da / Num. of mol.: 1 / Fragment: UNP residues 45-333 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83793
#4: Protein Cytochrome b6-f complex iron-sulfur subunit / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / ISP / RISP / Rieske iron-sulfur protein


Mass: 19422.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83794, EC: 1.10.9.1

-
Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17687.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit PetL / Cytochrome b6-f complex subunit VI


Mass: 3504.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83795
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit PetM / Cytochrome b6-f complex subunit VII


Mass: 3843.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83796
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit PetG / Cytochrome b6-f complex subunit V


Mass: 4016.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83797
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit PetN / Cytochrome b6-f complex subunit VIII


Mass: 3276.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83798

-
Non-polymers , 11 types, 32 molecules

#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#11: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#12: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#13: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#14: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical ChemComp-OZ2 / (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate


Mass: 704.912 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H69O10P
#16: Chemical ChemComp-1E2 / (2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside


Mass: 360.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20O11S
#17: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#18: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 6.18 Å3/Da / Density % sol: 80.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-20 MG/ML B6F DIMER MIXED WITH EQUAL VOLUME OF CRYSTALLIZATION BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONAPS 23-ID-B21.0332
Detector
TypeIDDetector
MARMOSAIC 300 mm CCD1CCD
MAR scanner 300 mm plate2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→48.52 Å / Num. all: 67115 / Num. obs: 67054 / % possible obs: 99.2 %
Reflection shellResolution: 2.8→2.85 Å / % possible all: 94.7

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
JBluIce-EPICSdata collection
RefinementResolution: 2.803→48.517 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.897 / SU ML: 0.43 / σ(F): 1.45 / Phase error: 26.09 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2718 3405 5.08 %
Rwork0.2484 --
obs0.2496 67054 99.21 %
all-67115 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.647 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.57 Å20 Å2
2--0.57 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.803→48.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 560 13 6959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057158
X-RAY DIFFRACTIONf_angle_d1.0589782
X-RAY DIFFRACTIONf_dihedral_angle_d15.0712608
X-RAY DIFFRACTIONf_chiral_restr0.1871077
X-RAY DIFFRACTIONf_plane_restr0.0041158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8026-2.84270.37661240.37352474X-RAY DIFFRACTION94
2.8427-2.88510.371290.36342547X-RAY DIFFRACTION97
2.8851-2.93020.37021600.34312549X-RAY DIFFRACTION99
2.9302-2.97820.37331500.34892598X-RAY DIFFRACTION99
2.9782-3.02960.34351220.33412602X-RAY DIFFRACTION99
3.0296-3.08460.33651650.31192579X-RAY DIFFRACTION99
3.0846-3.1440.3181420.30222640X-RAY DIFFRACTION99
3.144-3.20810.27891510.29972606X-RAY DIFFRACTION100
3.2081-3.27790.27791480.27712606X-RAY DIFFRACTION99
3.2779-3.35410.26151450.26362632X-RAY DIFFRACTION100
3.3541-3.43790.25631320.25492628X-RAY DIFFRACTION100
3.4379-3.53090.2761250.24812662X-RAY DIFFRACTION100
3.5309-3.63470.27051400.23542671X-RAY DIFFRACTION100
3.6347-3.7520.24571250.21522628X-RAY DIFFRACTION100
3.752-3.88610.22161610.20172656X-RAY DIFFRACTION100
3.8861-4.04160.23511380.20462643X-RAY DIFFRACTION100
4.0416-4.22540.24441410.20762673X-RAY DIFFRACTION100
4.2254-4.4480.22681380.19932686X-RAY DIFFRACTION100
4.448-4.72650.22581190.19132704X-RAY DIFFRACTION100
4.7265-5.09110.22051400.19732697X-RAY DIFFRACTION100
5.0911-5.60280.25891410.22022716X-RAY DIFFRACTION100
5.6028-6.41190.27781690.25022738X-RAY DIFFRACTION100
6.4119-8.07230.23791710.23092762X-RAY DIFFRACTION100
8.0723-48.52430.32441290.28772952X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -48.0265 Å / Origin y: 67.0967 Å / Origin z: 4.4455 Å
111213212223313233
T0.4129 Å20.08 Å20.0307 Å2-0.7724 Å2-0.0068 Å2--0.5144 Å2
L1.2874 °20.1516 °20.2274 °2-1.1064 °20.2039 °2--1.084 °2
S0.0986 Å °0.6112 Å °0.0262 Å °-0.1304 Å °-0.0408 Å °0.0986 Å °0.0132 Å °0.133 Å °-0.0484 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://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