- PDB-1w5c: Photosystem II from Thermosynechococcus elongatus -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1w5c
Title
Photosystem II from Thermosynechococcus elongatus
Components
(CYTOCHROME B559 ...) x 2
(PHOTOSYSTEM II ...) x 5
CYTOCHROME C-550
PHOTOSYSTEM Q(B) PROTEIN 1
UNASSIGNED SUBUNITS
Keywords
PHOTOSYNTHESIS / WATER OXIDATION / PHOTOSYSTEM / MEMBRANE PROTEIN
Function / homology
Function and homology information
cytochrome c-heme linkage / oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding ...cytochrome c-heme linkage / oxygen evolving activity / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / respiratory electron transport chain / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function
photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II CP43 reaction centre protein superfamily / Photosystem II CP43 reaction centre protein ...photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II CP43 reaction centre protein superfamily / Photosystem II CP43 reaction centre protein / Photosystem II CP47 reaction centre protein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PL9 / Photosystem II extrinsic protein V / Photosystem II protein D1 1 ...BETA-CAROTENE / CHLOROPHYLL A / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / PHEOPHYTIN A / Chem-PL9 / Photosystem II extrinsic protein V / Photosystem II protein D1 1 / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Cytochrome c-550 / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II CP47 reaction center protein Similarity search - Component
Biological species
THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.2 Å
A: PHOTOSYSTEM Q(B) PROTEIN 1 B: PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN C: PHOTOSYSTEM II CP43 PROTEIN D: PHOTOSYSTEM II REACTION CENTER D2 PROTEIN E: CYTOCHROME B559 ALPHA SUBUNIT F: CYTOCHROME B559 BETA SUBUNIT G: PHOTOSYSTEM Q(B) PROTEIN 1 H: PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN I: PHOTOSYSTEM II CP43 PROTEIN J: PHOTOSYSTEM II REACTION CENTER D2 PROTEIN K: CYTOCHROME B559 ALPHA SUBUNIT L: CYTOCHROME B559 BETA SUBUNIT O: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE P: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE S: PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN T: CYTOCHROME C-550 U: PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN V: CYTOCHROME C-550 X: UNASSIGNED SUBUNITS Y: UNASSIGNED SUBUNITS hetero molecules
A: PHOTOSYSTEM Q(B) PROTEIN 1 B: PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN C: PHOTOSYSTEM II CP43 PROTEIN D: PHOTOSYSTEM II REACTION CENTER D2 PROTEIN E: CYTOCHROME B559 ALPHA SUBUNIT F: CYTOCHROME B559 BETA SUBUNIT O: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE U: PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN V: CYTOCHROME C-550 X: UNASSIGNED SUBUNITS hetero molecules
G: PHOTOSYSTEM Q(B) PROTEIN 1 H: PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN I: PHOTOSYSTEM II CP43 PROTEIN J: PHOTOSYSTEM II REACTION CENTER D2 PROTEIN K: CYTOCHROME B559 ALPHA SUBUNIT L: CYTOCHROME B559 BETA SUBUNIT P: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE S: PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN T: CYTOCHROME C-550 Y: UNASSIGNED SUBUNITS hetero molecules
Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
-
Details
Sequence details
CHAINS O AND P CORRESPOND TO UNIPROT ENTRY PSBO_SYNEL (P55221), CHAINS U AND S CORRESPOND TO ...CHAINS O AND P CORRESPOND TO UNIPROT ENTRY PSBO_SYNEL (P55221), CHAINS U AND S CORRESPOND TO UNIPROT ENTRY PSBU_SNYEL (Q9F1L5). THE ELECTRON DENSITY FOR THESE REGIONS DO NOT ALLOW FOR UNAMBIGUOUS ASSIGNMENT OF SEQUENCE AND THEY ARE THEREFORE REPRESENTED BY RESIDUE TYPE UNK (UNKNOWN), WHICH IS REFLECTED IN THE CORRESPONDING SEQRES AND DBREF RECORDS. THE SEQUENCE IN FRAGMENTS MODELED AS POLY-ALA AND CA WAS ASSIGNED TENTATIVELY AND SHOULD BE TREATED WITH CAUTION.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 3
-
Sample preparation
Crystal
Density Matthews: 3.99 Å3/Da / Density % sol: 69.16 %
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.933 Å / Relative weight: 1
Reflection
Resolution: 3.2→50 Å / Num. obs: 133566 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.8
Reflection shell
Resolution: 3.2→3.26 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 56.1
-
Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
CCP4
phasing
SHARP
phasing
CNS
1
refinement
Refinement
Method to determine structure: MIRAS / Resolution: 3.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MLF Details: THE REFINEMENT PROCESS USED A NUMBER OF FAKE ATOMS AND RESIDUES WHOSE IDENTITY COULD NOT BE UNAMBIGUOUSLY ASSIGNED. THESE WERE REMOVED FROM THE STRUCTURE THAT WAS DEPOSITED TO THE PDB. THE ...Details: THE REFINEMENT PROCESS USED A NUMBER OF FAKE ATOMS AND RESIDUES WHOSE IDENTITY COULD NOT BE UNAMBIGUOUSLY ASSIGNED. THESE WERE REMOVED FROM THE STRUCTURE THAT WAS DEPOSITED TO THE PDB. THE REFINEMENT STATISTICS HAVE NOT BEEN INCLUDED HERE, SINCE THEY DO NOT ACCURATELY REFLECT THE REFINEMENT PROCESS FOR THE AVAILABLE STRUCTURE
Num. reflection
% reflection
obs
107320
75.6 %
Displacement parameters
Biso mean: 45.23 Å2
Baniso -1
Baniso -2
Baniso -3
1-
33.02 Å2
0 Å2
0 Å2
2-
-
-5.16 Å2
0 Å2
3-
-
-
-27.85 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.78 Å
0.76 Å
Luzzati d res low
-
10 Å
Luzzati sigma a
0.76 Å
0.65 Å
Refinement step
Cycle: LAST / Resolution: 3.2→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
31578
0
4036
0
35614
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.014
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.954
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
19.9
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
1.98
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
X-RAY DIFFRACTION
c_mcangle_it
X-RAY DIFFRACTION
c_scbond_it
X-RAY DIFFRACTION
c_scangle_it
Refine LS restraints NCS
NCS model details: RESTRAINTS
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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