3PCQ

Femtosecond X-ray protein Nanocrystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.98 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.252

Literature

Macromolecules
Sequence Display for 3PCQ

Classification: PHOTOSYNTHESIS

Total Structure Weight: 359828.38

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem I P700 chlorophyll a apoprotein A1 A 755 Thermosynechococcus elongatus EC#: 1.1.1.239 IUBMB 1.97.1.12 IUBMB
Gene Name(s): psaA tlr0731
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I P700 chlorophyll a apoprotein A2 B 740 Thermosynechococcus elongatus EC#: 1.97.1.12 IUBMB
Gene Name(s): psaB tlr0732
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I iron-sulfur center C 80 Thermosynechococcus elongatus EC#: 1.97.1.12 IUBMB
Gene Name(s): psaC tsl1013
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit II D 138 Thermosynechococcus elongatus Gene Name(s): psaD tll1724
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit IV E 75 Thermosynechococcus elongatus Gene Name(s): psaE tsl1567
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit III F 164 Thermosynechococcus elongatus Gene Name(s): psaF tlr2411
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit VIII I 38 Thermosynechococcus elongatus Gene Name(s): psaI tsr2405
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit IX J 41 Thermosynechococcus elongatus Gene Name(s): psaJ tsr2412
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit PsaK K 83 Thermosynechococcus elongatus Gene Name(s): psaK tsr2273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit XI L 154 Thermosynechococcus elongatus Mutation: S143L
Gene Name(s): psaL tlr2404
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I reaction center subunit XII M 31 Thermosynechococcus elongatus Gene Name(s): psaM tsr0197
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem I 4.8K protein X 35 Thermosynechococcus elongatus Gene Name(s): tsr0813
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem I


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLA
Query on CLA

A, B, F, J, K, L, M, X CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMG
Query on LMG

B 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LHG
Query on LHG

A, B 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

A, B, F, I, J, L, M BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PQN
Query on PQN

A, B PHYLLOQUINONE
4-NAPHTHOQUINONE, (Synonym)
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, C IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.98 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.252
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 281.00 α = 90.00
b = 281.00 β = 90.00
c = 165.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-10-21
  • Released Date: 2011-02-02
  • Deposition author(s): Chapman, H.N., Fromme, P., Barty, A., White, T.A., Kirian, R.A., Aquila, A., Hunter, M.S., Schulz, J., Deponte, D.P., Weierstall, U., Doak, R.B., Maia, F.R.N.C., Martin, A.V., Schlichting, I., Lomb, L., Coppola, N., Shoeman, R.L., Epp, S.W., Hartmann, R., Rolles, D., Rudenko, A., Foucar, L., Kimmel, N., Weidenspointner, G., Holl, P., Liang, M., Barthelmess, M., Caleman, C., Boutet, S., Bogan, M.J., Krzywinski, J., Bostedt, C., Bajt, S., Gumprecht, L., Rudek, B., Erk, B., Schmidt, C., Homke, A., Reich, C., Pietschner, D., Struder, L., Hauser, G., Gorke, H., Ullrich, J., Herrmann, S., Schaller, G., Schopper, F., Soltau, H., Kuhnel, K.-U., Messerschmidt, M., Bozek, J.D., Hau-Riege, S.P., Frank, M., Hampton, C.Y., Sierra, R., Starodub, D., Williams, G.J., Hajdu, J., Timneanu, N., Seibert, M.M., Andreasson, J., Rocker, A., Jonsson, O., Svenda, M., Stern, S., Nass, K., Andritschke, R., Schroter, C.-D., Krasniqi, F., Bott, M., Schmidt, K.E., Wang, X., Grotjohann, I., Holton, J.M., Barends, T.R.M., Neutze, R., Marchesini, S., Fromme, R., Schorb, S., Rupp, D., Adolph, M., Gorkhover, T., Andersson, I., Hirsemann, H., Potdevin, G., Graafsma, H., Nilsson, B., Spence, J.C.H.

Revision History

  • Version 1_0: 2011-02-02

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Source and taxonomy, Version format compliance

  • Version 1_2: 2012-02-08

    Type: Data collection

  • Version 1_3: 2012-07-25

    Type: Non-polymer description