3PCQ Photosynthesis date Oct 21, 2010
title Femtosecond X-Ray Protein Nanocrystallography
authors H.N.Chapman, P.Fromme, A.Barty, T.A.White, R.A.Kirian, A.Aquila, M.S.Hunter, J.Schulz, D.P.Deponte, U.Weierstall, R.B.Doak, F.R.N A.V.Martin, I.Schlichting, L.Lomb, N.Coppola, R.L.Shoeman, S.W.E R.Hartmann, D.Rolles, A.Rudenko, L.Foucar, N.Kimmel, G.Weidenspo P.Holl, M.Liang, M.Barthelmess, C.Caleman, S.Boutet, M.J.Bogan, J.Krzywinski, C.Bostedt, S.Bajt, L.Gumprecht, B.Rudek, B.Erk, C.S A.Homke, C.Reich, D.Pietschner, L.Struder, G.Hauser, H.Gorke, J.U S.Herrmann, G.Schaller, F.Schopper, H.Soltau, K.U.Kuhnel, M.Messerschmidt, J.D.Bozek, S.P.Hau-Riege, M.Frank, C.Y.Hampton R.Sierra, D.Starodub, G.J.Williams, J.Hajdu, N.Timneanu, M.M.Sei J.Andreasson, A.Rocker, O.Jonsson, M.Svenda, S.Stern, K.Nass, R.Andritschke, C.D.Schroter, F.Krasniqi, M.Bott, K.E.Schmidt, X I.Grotjohann, J.M.Holton, T.R.M.Barends, R.Neutze, S.Marchesini R.Fromme, S.Schorb, D.Rupp, M.Adolph, T.Gorkhover, I.Andersson, H.Hirsemann, G.Potdevin, H.Graafsma, B.Nilsson, J.C.H.Spence
compound source
Molecule: Photosystem I P700 Chlorophyll A Apoprotein A1
Chain: A
Synonym: Psaa
 Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I P700 Chlorophyll A Apoprotein A2
Chain: B
Synonym: Psab
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Iron-Sulfur Center
Chain: C
Synonym: 9 Kda Polypeptide, Psi-C, Photosystem I Subunit Vi
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit II
Chain: D
Synonym: Photosystem I 16 Kda Polypeptide, Psi-D
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit Iv
Chain: E
Synonym: Photosystem I 8.1 Kda Protein, P30 Protein
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit III
Chain: F
Synonym: Psi-F
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit Viii
Chain: I
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit Ix
Chain: J
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit Psak
Chain: K
Synonym: Light-Harvesting 8.0 Kda Polypeptide, Photosystem X;
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit Xi
Chain: L
Synonym: Psi Subunit V, Psi-L
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I Reaction Center Subunit Xii
Chain: M
Synonym: Psi-M
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1

Molecule: Photosystem I 4.8k Protein
Chain: X
Organism_scientific: Thermosynechococcus Elongatus
Organism_taxid: 197221
Strain: Bp-1
symmetry Space Group: P 63
R_factor 0.252 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
281.000 281.000 165.200 90.00 90.00 120.00
method X-Ray Diffractionresolution 8.98 Å
ligand BCR, CA, CLA, LHG, LMG, PQN, SF4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • electron transfer activity


    • B
  • electron transfer activity


    • C


    D


    E


    F


    I


    J


    K


    L


    M


    X


    Primary referenceFemtosecond X-ray protein nanocrystallography., Chapman HN, Fromme P, Barty A, White TA, Kirian RA, Aquila A, Hunter MS, Schulz J, Deponte DP, Weierstall U, Doak RB, Maia FR, Martin AV, Schlichting I, Lomb L, Coppola N, Shoeman RL, Epp SW, Hartmann R, Rolles D, Rudenko A, Foucar L, Kimmel N, Weidenspointner G, Holl P, Liang M, Barthelmess M, Caleman C, Boutet S, Bogan MJ, 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 KU, Messerschmidt M, Bozek JD, Hau-Riege SP, Frank M, Hampton CY, Sierra RG, Starodub D, Williams GJ, Hajdu J, Timneanu N, Seibert MM, Andreasson J, Rocker A, Jonsson O, Svenda M, Stern S, Nass K, Andritschke R, Schroter CD, Krasniqi F, Bott M, Schmidt KE, Wang X, Grotjohann I, Holton JM, Barends TR, 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 JC, Nature. 2011 Feb 3;470(7332):73-7. PMID:21293373
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (537 Kb) [Save to disk]
  • Biological Unit Coordinates (3pcq.pdb1.gz) 1416 Kb
  • LPC: Ligand-Protein Contacts for 3PCQ
  • CSU: Contacts of Structural Units for 3PCQ
  • Structure Factors (119 Kb)
  • Retrieve 3PCQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PCQ from S2C, [Save to disk]
  • Re-refined 3pcq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3PCQ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3PCQ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3PCQ, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pcq_K] [3pcq_L] [3pcq_D] [3pcq_M] [3pcq_I] [3pcq_A] [3pcq_B] [3pcq_F] [3pcq] [3pcq_C] [3pcq_X] [3pcq_J] [3pcq_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3PCQ
  • Community annotation for 3PCQ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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