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- PDB-6zxs: Cold grown Pea Photosystem I -

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Basic information

Entry
Database: PDB / ID: 6zxs
TitleCold grown Pea Photosystem I
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
  • Chlorophyll a-b binding protein, chloroplastic
  • Lhca1
  • Photosystem I iron-sulfur center
  • PsaD
  • PsaE
  • PsaG
  • PsaL domain-containing protein
KeywordsPHOTOSYNTHESIS
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis ...chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding
Similarity search - Function
4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...4Fe-4S dicluster domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / 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 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Chem-ZEX / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit III / Photosystem I reaction center subunit IX / PSI subunit V / PSI-K / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCaspy, I. / Borovikova-Sheinker, A. / Subramanyam, R. / Nelson, N.
Funding support Israel, India, 2items
OrganizationGrant numberCountry
Israel Science Foundation569/17 Israel
The University Grants Committee, Research Grants Council (RGC)2716/17 India
CitationJournal: To Be Published
Title: Structure of cold grown pea Photosystem I
Authors: Nelson, N. / Caspy, I. / Subramanyam, R.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: PsaD
E: PsaE
F: Photosystem I reaction center subunit III
G: PsaG
H: Photosystem I reaction center subunit VI
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X psaK
L: PsaL domain-containing protein
1: Lhca1
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)547,513256
Polymers357,57416
Non-polymers189,940240
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.197, 201.786, 213.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / / PSI-A / PsaA


Mass: 82571.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0F6NFW5, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82381.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0F6NGI2, photosystem I

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Protein , 7 types, 7 molecules CDEGL12

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


Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: P10793, photosystem I
#4: Protein PsaD


Mass: 16041.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS
#5: Protein PsaE


Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS
#7: Protein PsaG


Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS
#12: Protein PsaL domain-containing protein


Mass: 16564.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: E1C9L1
#13: Protein Lhca1


Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22845.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: Q41038

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Photosystem I reaction center subunit ... , 5 types, 5 molecules FHIJK

#6: Protein Photosystem I reaction center subunit III /


Mass: 17137.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0M3KL12
#8: Protein Photosystem I reaction center subunit VI /


Mass: 9491.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0M3KL10
#9: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 3296.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: P17227
#10: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4767.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: D5MAL3
#11: Protein Photosystem I reaction center subunit X psaK /


Mass: 7988.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: E1C9L3

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Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34

#15: Protein Chlorophyll a-b binding protein 3, chloroplastic / LHCII type III CAB-3


Mass: 24139.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: Q32904
#16: Protein Chlorophyll a-b binding protein P4, chloroplastic / LHCI type III CAB-P4


Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: Q9SQL2

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Sugars , 2 types, 14 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#26: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 13 types, 226 molecules

#17: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 138 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: 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
#20: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 536.873 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C40H56
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#24: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C45H86O10
#25: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#27: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#28: Chemical ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56O2
#29: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H56O2
#30: Chemical
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#31: Chemical ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4

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Details

Has ligand of interestN

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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: 5.73 Å3/Da / Density % sol: 78.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: di-potassium phosphate, Tris, PEG400, glycerol, L-glutathione, octyl glucose neopentyl glycol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 162077 / % possible obs: 98.8 % / Redundancy: 7 % / Biso Wilson estimate: 96.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.326 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 7998 / CC1/2: 0.066

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L8R

5l8r


Resolution: 3→49.63 Å / SU ML: 0.4895 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.3856
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2697 3139 2.09 %
Rwork0.2394 147400 -
obs0.24 150539 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.94 Å2
Refinement stepCycle: LAST / Resolution: 3→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25318 0 12105 0 37423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004839531
X-RAY DIFFRACTIONf_angle_d1.753855784
X-RAY DIFFRACTIONf_chiral_restr0.08144952
X-RAY DIFFRACTIONf_plane_restr0.00747246
X-RAY DIFFRACTIONf_dihedral_angle_d24.968616161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.050.5123500.46982582X-RAY DIFFRACTION35.63
3.05-3.10.4485470.42463865X-RAY DIFFRACTION52.79
3.1-3.150.4211180.425065X-RAY DIFFRACTION70.11
3.15-3.210.42471300.41016452X-RAY DIFFRACTION89.33
3.21-3.270.41361180.39637002X-RAY DIFFRACTION96.14
3.27-3.340.38471680.36677120X-RAY DIFFRACTION98.31
3.34-3.410.35411580.35377149X-RAY DIFFRACTION98.9
3.41-3.490.37481880.33187160X-RAY DIFFRACTION98.9
3.49-3.570.35861670.30397167X-RAY DIFFRACTION99.26
3.57-3.670.32971680.28347178X-RAY DIFFRACTION98.84
3.67-3.780.32531630.26537174X-RAY DIFFRACTION98.97
3.78-3.90.28731650.2537193X-RAY DIFFRACTION98.96
3.9-4.040.29161350.23557199X-RAY DIFFRACTION98.46
4.04-4.20.24981090.21536650X-RAY DIFFRACTION90.83
4.2-4.390.23481490.19127207X-RAY DIFFRACTION98.8
4.39-4.630.21161670.18397265X-RAY DIFFRACTION99.48
4.63-4.910.20581830.18077248X-RAY DIFFRACTION99.6
4.91-5.290.24561680.18197316X-RAY DIFFRACTION99.53
5.29-5.830.22951550.19657325X-RAY DIFFRACTION99.48
5.83-6.670.23111670.19947333X-RAY DIFFRACTION99.39
6.67-8.390.24591280.20957109X-RAY DIFFRACTION94.86
8.39-49.630.23851380.23957641X-RAY DIFFRACTION98.93
Refinement TLS params.Method: refined / Origin x: 14.8200063301 Å / Origin y: 7.42920184276 Å / Origin z: -42.0413916319 Å
111213212223313233
T0.756200465857 Å20.0786005891418 Å2-0.111985453258 Å2-0.802614746329 Å20.0403981803286 Å2--0.779545207701 Å2
L0.510064327155 °2-0.0207468862475 °2-0.00642415912008 °2-1.10112828149 °2-0.0385908839667 °2--0.545431013089 °2
S-0.0172306987474 Å °-0.0569301665063 Å °0.0665382662114 Å °-0.0365106538684 Å °0.0538269665558 Å °0.0963349401729 Å °-0.0406717202413 Å °0.00534215178536 Å °2.86020397659E-5 Å °
Refinement TLS groupSelection details: all

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