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- PDB-6hqb: Monomeric cyanobacterial photosystem I -

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Basic information

Entry
Database: PDB / ID: 6hqb
TitleMonomeric cyanobacterial photosystem I
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Crystal structure / Cyanobacteria / Membrane complexes / Photosynthesis / Photosystem I / Synechocystis
Function / homologyPhotosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaB / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein PsaC / Photosystem I PsaK, reaction centre / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I, reaction centre subunit XI ...Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I PsaA/PsaB, conserved site / Photosystem I PsaB / Electron transport accessory-like domain superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein PsaC / Photosystem I PsaK, reaction centre / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Photosystem I, reaction centre subunit XI / Photosystem I PsaD / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaA/PsaB superfamily / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit PsaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaF, reaction centre subunit III / Photosystem I psaA/psaB protein / PsaD / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Photosystem I psaG and psaK proteins signature. / Photosystem I psaA and psaB proteins signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S dicluster domain / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit III / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I psaG / psaK / Photosystem I PsaG/PsaK protein / Photosystem I PsaA/PsaB / Photosystem I reaction centre subunit VIII / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaM, reaction centre superfamily / plasma membrane-derived photosystem I / photosystem I / photosynthetic electron transport in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chlorophyll binding / thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / protein-chromophore linkage / electron transfer activity / magnesium ion binding / integral component of membrane / metal ion binding / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / un:p29254: / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK 2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Function and homology information
Specimen sourceSynechocystis sp. (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 4 Å resolution
AuthorsNetzer-El, S.Y. / Nelson, N. / Caspy, I.
CitationJournal: Front Plant Sci / Year: 2018
Title: Crystal Structure of Photosystem I Monomer From Synechocystis PCC 6803.
Authors: Netzer-El, S.Y. / Caspy, I. / Nelson, N.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2018 / Release: Jan 16, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 16, 2019Structure modelrepositoryInitial release
1.1Jan 30, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK 2
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)349,063141
Polyers246,44211
Non-polymers102,621130
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)124.322, 178.658, 181.446
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein/peptide Photosystem I P700 chlorophyll a apoprotein A1 / / PsaA


Mass: 83036.398 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P29254, photosystem I
#2: Protein/peptide Photosystem I P700 chlorophyll a apoprotein A2 / / PsaB


Mass: 81369.531 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P29255, photosystem I

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8706.064 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P32422, photosystem I

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJKLM

#4: Protein/peptide Photosystem I reaction center subunit II / / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15663.749 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P19569
#5: Protein/peptide Photosystem I reaction center subunit IV / / Photosystem I 8.1 kDa protein / p30 protein


Mass: 7680.478 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P12975
#6: Protein/peptide Photosystem I reaction center subunit III / / PSI-F


Mass: 15791.086 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P29256
#7: Protein/peptide Photosystem I reaction center subunit VIII /


Mass: 4414.148 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55330
#8: Protein/peptide Photosystem I reaction center subunit IX /


Mass: 4535.415 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55329
#9: Protein/peptide Photosystem I reaction center subunit PsaK 2 / / Photosystem I subunit X 2


Mass: 7339.811 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P74564
#10: Protein/peptide Photosystem I reaction center subunit XI / / PSI subunit V / PSI-L


Mass: 14523.503 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P37277
#11: Protein/peptide Photosystem I reaction center subunit XII / / PSI-M


Mass: 3382.063 Da / Num. of mol.: 1
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (Cyanobacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72986

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Non-polymers , 14 types, 130 molecules

#12: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 93 / Formula: C55H72MgN4O5 / Chlorophyll a
#13: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Formula: C31H46O2 / Phytomenadione
#14: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Formula: Fe4S4 / Iron–sulfur cluster
#15: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 14 / Formula: C40H56 / Beta-Carotene
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Formula: C38H75O10P
#17: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Formula: C40H52O2
#18: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl / Chloride
#19: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 2 / Formula: C40H54O / Echinenone
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Formula: C45H86O10
#21: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Formula: C41H78O12S
#22: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#23: Chemical ChemComp-C7Z / (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 2 / Formula: C40H56O2
#24: Chemical ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Mass: 510.615 Da / Num. of mol.: 1 / Formula: C24H46O11 / Comment: detergent *YM
#25: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone, 3'-OH-Echinenone


Mass: 566.856 Da / Num. of mol.: 1 / Formula: C40H54O2 / 3'-Hydroxyechinenone

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.35 / Density percent sol: 69.9 %
Crystal growTemp: 277 K / Method: vapor diffusion, sitting drop
Details: KCl, MES-NaOH, PEG 3350, sulfoquinovosyldiacylglycerol or Jeffamine M-600

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Data collection

Diffraction
IDMean temperatureCrystal IDSerial crystal experiment
1821N
2821N
Source
SourceSiteBeamlineIdWavelength
SYNCHROTRONSLS X06DA10.999
SYNCHROTRONESRF ID23-220.873
Detector
TypeIdDetectorCollection date
DECTRIS EIGER X 16M1PIXEL2017-09-17
DECTRIS PILATUS 2M2PIXEL2017-07-08
Radiation
IdDiffraction protocolMonochromatic or laue m lScattering typeWavelength ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelengthRelative weight
10.9991.0
20.8731.0
ReflectionD resolution high: 4 Å / D resolution low: 50 Å / Number obs: 34852 / Rpim I all: 0.092 / NetI over sigmaI: 4.9 / Redundancy: 24 % / Percent possible obs: 99.7
Reflection shellHighest resolution: 4 Å / Lowest resolution: 50 Å / Rpim I all: 0.437

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Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.5 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 34.87 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.295 / R factor R work: 0.2552 / R factor obs: 0.256 / Highest resolution: 4 Å / Lowest resolution: 49.289 Å / Number reflection R free: 584 / Number reflection obs: 30859 / Percent reflection R free: 1.89 / Percent reflection obs: 88.69
Refine hist #LASTHighest resolution: 4 Å / Lowest resolution: 49.289 Å
Number of atoms included #LASTProtein: 17427 / Nucleic acid: 0 / Ligand: 6141 / Solvent: 0 / Total: 23568
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424882
X-RAY DIFFRACTIONf_angle_d1.29935241
X-RAY DIFFRACTIONf_dihedral_angle_d19.02113495
X-RAY DIFFRACTIONf_chiral_restr0.0453078
X-RAY DIFFRACTIONf_plane_restr0.0074272
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
4.00010.28930.26084.4024126533164.00
4.40240.30400.23155.0389136763890.00
5.03890.27810.26656.34641718502100.00
6.34640.30330.261349.29251518804100.00
Refine TLSMethod: refined / L11: 1.2987 deg.2 / L12: 0.3766 deg.2 / L13: 0.4673 deg.2 / L22: 1.6788 deg.2 / L23: -0.0258 deg.2 / L33: 0.8693 deg.2 / S11: -0.3249 Å deg. / S12: -0.3971 Å deg. / S13: -0.0202 Å deg. / S21: 0.7225 Å deg. / S22: 0.0853 Å deg. / S23: -0.6015 Å deg. / S31: -0.3166 Å deg. / S32: 0.8703 Å deg. / S33: -1.7852 Å deg. / T11: -0.439 Å2 / T12: -0.5508 Å2 / T13: -0.3488 Å2 / T22: -0.5817 Å2 / T23: -0.0315 Å2 / T33: -0.0585 Å2 / Origin x: -40.0247 Å / Origin y: -23.0823 Å / Origin z: -34.8269 Å
Refine TLS groupSelection details: all

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