ISDA

Deposition Date 2013-01-27

Release Date 2013-02-20

Last Version Date 2024-10-30

Entry Detail

PDB ID:

4IXQ

Keywords:

PHOTOSYNTHESIS

Title:

RT fs X-ray diffraction of Photosystem II, dark state

Biological Source:

Source Organism:

Thermosynechococcus elongatus (Taxon ID: 197221)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

5.70 Å

R-Value Free:

0.31

R-Value Work:

0.27

R-Value Observed:

0.27

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem Q(B) protein 1
Gene (Uniprot):psbA1
Chain IDs:A, U (auth: a)
Chain Length:360
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P0A444 Pfam ID:PF00124 EC:1.10.3.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II core light harvesting protein
Gene (Uniprot):psbB
Chain IDs:B, V (auth: b)
Chain Length:510
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIQ1 Pfam ID:PF00421

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 protein
Gene (Uniprot):psbC
Chain IDs:C, W (auth: c)
Chain Length:461
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIF8 Pfam ID:PF00421

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD1, psbD2
Chain IDs:D, X (auth: d)
Chain Length:352
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8CM25 Pfam ID:PF00124 EC:1.10.3.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Y (auth: e)
Chain Length:84
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIP0 Pfam ID:PF00283, PF00284

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, Z (auth: f)
Chain Length:45
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIN9 Pfam ID:PF00283

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), AA (auth: h)
Chain Length:66
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DJ43 Pfam ID:PF00737

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), BA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DJZ6 Pfam ID:PF02532

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), CA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P59087 Pfam ID:PF01788

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), DA (auth: k)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q9F1K9 Pfam ID:PF02533

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), EA (auth: l)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIN8 Pfam ID:PF02419

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), FA (auth: m)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DHA7 Pfam ID:PF05151

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), GA (auth: o)
Chain Length:272
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P0A431 Pfam ID:PF01716

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:N (auth: T), HA (auth: t)
Chain Length:32
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DIQ0 Pfam ID:PF01405

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:O (auth: U), IA (auth: u)
Chain Length:134
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q9F1L5 Pfam ID:PF06514

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:P (auth: V), JA (auth: v)
Chain Length:163
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:P0A386 Pfam ID:PF14495

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:R (auth: X), LA (auth: x)
Chain Length:41
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q9F1R6 Pfam ID:PF06596

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Y
Chain IDs:T (auth: Y), NA (auth: G)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:S (auth: Z), MA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DHJ2 Pfam ID:PF01737

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein ycf12
Gene (Uniprot):psb30
Chain IDs:Q (auth: y), KA (auth: g)
Chain Length:46
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus

UniProt ID:Q8DJI1 Pfam ID:PF05969

Ligand Molecules

BCR

BCT

CLA

DGD

FE2

HEM

LHG

LMG

LMT

OEC

PHO

PL9

SQD

Primary Citation

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Kern, J, Alonso-Mori, R, Tran, R, Hattne, J, Gildea, R.J, Echols, N, Glockner, C, Hellmich, J, Laksmono, H, Sierra, R.G, Lassalle-Kaiser, B, Koroidov, S, Lampe, A, Han, G, Gul, S, Difiore, D, Milathianaki, D, Fry, A.R, Miahnahri, A, Schafer, D.W, Messerschmidt, M, Seibert, M.M, Koglin, J.E, Sokaras, D, Weng, T.C, Sellberg, J, Latimer, M.J, Grosse-Kunstleve, R.W, Zwart, P.H, White, W.E, Glatzel, P, Adams, P.D, Bogan, M.J, Williams, G.J, Boutet, S, Messinger, J, Zouni, A, Sauter, N.K, Yachandra, V.K, Bergmann, U, Yano, J.Show

Science 340 491 495 (2013)

PMID: 23413188 DOI: 10.1126/science.1234273

Abstact

Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD-XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.

Legend

Protein

Chemical

Disease

Primary Citation of related structures