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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 / Photosystem I / Synechocystis
Function / homology
Function and homology information


plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / SH3 type barrels. - #50 ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Alpha-Beta Plaits - #20 / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL A / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...beta,beta-carotene-4,4'-dione / BETA-CAROTENE / Chem-C7Z / CHLOROPHYLL A / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / 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
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsNetzer-El, S.Y. / Nelson, N. / Caspy, I.
Funding support Belgium, 1items
OrganizationGrant numberCountry
European Research Council293579 Belgium
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.
History
DepositionSep 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._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
Polymers246,44211
Non-polymers102,621130
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP212121

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Components

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

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


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


Mass: 81369.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P29255, photosystem I

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

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


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


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


Mass: 15791.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
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 method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
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 method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55329
#9: Protein Photosystem I reaction center subunit PsaK 2 / / Photosystem I subunit X 2


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


Mass: 14523.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
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 method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72986

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Protein / Sugars , 2 types, 2 molecules C

#24: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Photosystem I iron-sulfur center / / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8706.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P32422, photosystem I

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Non-polymers , 13 types, 129 molecules

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


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


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#14: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C40H56
#16: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin / Canthaxanthin


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


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


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


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 / Source method: obtained synthetically / Formula: C41H78O12S
#22: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#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 / Source method: obtained synthetically / Formula: C40H56O2
#25: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone, 3'-OH-Echinenone / 3'-Hydroxyechinenone


Mass: 566.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O2

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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 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 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 temperature (K)Crystal-IDSerial crystal experiment
1821N
2821N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA10.999
SYNCHROTRONESRF ID23-220.873
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELSep 17, 2017
DECTRIS PILATUS 2M2PIXELJul 8, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9991
20.8731
ReflectionResolution: 4→50 Å / Num. obs: 34852 / % possible obs: 99.7 % / Redundancy: 24 % / Rpim(I) all: 0.092 / Net I/σ(I): 4.9
Reflection shellResolution: 4→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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→49.289 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 584 1.89 %
Rwork0.2552 --
obs0.256 30859 88.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→49.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17427 0 6141 0 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
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.40240.28931260.26085331X-RAY DIFFRACTION64
4.4024-5.03890.3041360.23157638X-RAY DIFFRACTION90
5.0389-6.34640.27811710.26658502X-RAY DIFFRACTION100
6.3464-49.29250.30331510.26138804X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -40.0247 Å / Origin y: -23.0823 Å / Origin z: -34.8269 Å
111213212223313233
T-0.439 Å2-0.5508 Å2-0.3488 Å2--0.5817 Å2-0.0315 Å2---0.0585 Å2
L1.2987 °20.3766 °20.4673 °2-1.6788 °2-0.0258 °2--0.8693 °2
S-0.3249 Å °-0.3971 Å °-0.0202 Å °0.7225 Å °0.0853 Å °-0.6015 Å °-0.3166 Å °0.8703 Å °-1.7852 Å °
Refinement TLS groupSelection details: all

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