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- PDB-1w5c: Photosystem II from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 1w5c
TitlePhotosystem II from Thermosynechococcus elongatus
Components
  • (CYTOCHROME B559 ...) x 2
  • (PHOTOSYSTEM II ...) x 5
  • CYTOCHROME C-550
  • PHOTOSYSTEM Q(B) PROTEIN 1
  • UNASSIGNED SUBUNITS
KeywordsPHOTOSYNTHESIS / WATER OXIDATION / PHOTOSYSTEM / MEMBRANE PROTEIN
Function / homology
Function and homology information


cytochrome c-heme linkage / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding ...cytochrome c-heme linkage / oxygen evolving activity / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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 speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.2 Å
AuthorsBiesiadka, J. / Loll, B. / Kern, J. / Irrgang, K.-D. / Saenger, W.
CitationJournal: Phys.Chem.Chem.Phys. / Year: 2004
Title: Crystal Structure of Cyanobacterial Photosystem II at 3.2 A Resolution: A Closer Look at the Mn- Cluster
Authors: Biesiadka, J. / Loll, B. / Kern, J. / Irrgang, K.-D. / Zouni, A.
History
DepositionAug 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.2Jan 8, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)620,399112
Polymers548,77720
Non-polymers71,62292
Water0
1
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


Theoretical massNumber of molelcules
Total (without water)310,20056
Polymers274,38810
Non-polymers35,81146
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72600 Å2
ΔGint-344.4 kcal/mol
Surface area135320 Å2
MethodPQS
2
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


Theoretical massNumber of molelcules
Total (without water)310,20056
Polymers274,38810
Non-polymers35,81146
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area68780 Å2
ΔGint-312.8 kcal/mol
Surface area135460 Å2
MethodPQS
Unit cell
Length a, b, c (Å)127.517, 224.612, 305.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules AGTVXY

#1: Protein PHOTOSYSTEM Q(B) PROTEIN 1 / PHOTOSYSTEM II PROTEIN D1


Mass: 39762.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: P0A444
#9: Protein CYTOCHROME C-550 / PSII SUBUNIT PSBV / CYTOCHROME C550 / LOW POTENTIAL CYTOCHROME C


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: P56150, UniProt: P0A386*PLUS
#10: Protein UNASSIGNED SUBUNITS


Mass: 30570.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)

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PHOTOSYSTEM II ... , 5 types, 10 molecules BHCIDJOPSU

#2: Protein PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN / / PSII SUBUNIT PSBB


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: Q8DIQ1
#3: Protein PHOTOSYSTEM II CP43 PROTEIN / / PSII SUBUNIT PSBC


Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: Q8DIF8
#4: Protein PHOTOSYSTEM II REACTION CENTER D2 PROTEIN / / PSII SUBUNIT PSBD


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: Q8CM25
#7: Protein PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE / / PSII SUBUNIT PSBO / MSP


Mass: 15251.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
#8: Protein PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN / / PSII SUBUNIT PSBU / PS II COMPLEX 12KDA EXTRINSIC PROTEIN / PSII-U


Mass: 8528.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)

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CYTOCHROME B559 ... , 2 types, 4 molecules EKFL

#5: Protein CYTOCHROME B559 ALPHA SUBUNIT / PSII SUBUNIT PSBE / PSII REACTION CENTER SUBUNIT V


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: P12238, UniProt: Q8DIP0*PLUS
#6: Protein/peptide CYTOCHROME B559 BETA SUBUNIT / PSII SUBUNIT PSBF / PSII REACTION CENTER SUBUNIT VI


Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / References: UniProt: P12239, UniProt: Q8DIN9*PLUS

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Non-polymers , 8 types, 92 molecules

#11: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#12: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#13: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#14: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#16: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#17: Chemical ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#18: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Details

Sequence detailsCHAINS 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.99 Å3/Da / Density % sol: 69.16 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 56.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
SHARPphasing
CNS1refinement
RefinementMethod 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
obs107320 75.6 %
Displacement parametersBiso mean: 45.23 Å2
Baniso -1Baniso -2Baniso -3
1-33.02 Å20 Å20 Å2
2---5.16 Å20 Å2
3----27.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.78 Å0.76 Å
Luzzati d res low-10 Å
Luzzati sigma a0.76 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31578 0 4036 0 35614
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.954
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS

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