5h2f

X-ray diffraction
2.2Å resolution

Crystal structure of the PsbM-deletion mutant of photosystem II

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
Photosystem II protein D1 1 Chains: A, a
Molecule details ›
Chains: A, a
Length: 334 amino acids
Theoretical weight: 37.06 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: P0A444 (Residues: 11-344; Coverage: 93%)
Gene names: psbA-1, psbA1, tlr1843
Sequence domains: Photosynthetic reaction centre protein
Photosystem II CP47 reaction center protein Chains: B, b
Molecule details ›
Chains: B, b
Length: 505 amino acids
Theoretical weight: 56.1 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DIQ1 (Residues: 2-506; Coverage: 99%)
Gene names: psbB, tlr1530
Photosystem II CP43 reaction center protein Chains: C, c
Molecule details ›
Chains: C, c
Length: 455 amino acids
Theoretical weight: 49.67 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DIF8 (Residues: 7-461; Coverage: 99%)
Gene names: psbC, tlr1631
Sequence domains: Photosystem II protein
Structure domains: photosystem ii from thermosynechococcus elongatus
Photosystem II D2 protein Chains: D, d
Molecule details ›
Chains: D, d
Length: 342 amino acids
Theoretical weight: 38.4 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8CM25 (Residues: 11-352; Coverage: 97%)
Gene names: psbD1, psbD2, tlr0455, tlr1630
Sequence domains: Photosynthetic reaction centre protein
Cytochrome b559 subunit alpha Chains: E, e
Molecule details ›
Chains: E, e
Length: 80 amino acids
Theoretical weight: 9.22 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DIP0 (Residues: 5-84; Coverage: 95%)
Gene names: psbE, tsr1541
Sequence domains:
Structure domains: Photosystem II cytochrome b559, alpha subunit
Cytochrome b559 subunit beta Chains: F, f
Molecule details ›
Chains: F, f
Length: 33 amino acids
Theoretical weight: 3.78 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DIN9 (Residues: 13-45; Coverage: 73%)
Gene names: psbF, tsr1542
Photosystem II reaction center protein H Chains: H, h
Molecule details ›
Chains: H, h
Length: 63 amino acids
Theoretical weight: 7.06 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DJ43 (Residues: 2-64; Coverage: 96%)
Gene names: psbH, tsl1386
Sequence domains: Photosystem II 10 kDa phosphoprotein
Structure domains: Photosystem II reaction center protein H
Photosystem II reaction center protein I Chains: I, i
Molecule details ›
Chains: I, i
Length: 36 amino acids
Theoretical weight: 4.2 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DJZ6 (Residues: 1-36; Coverage: 95%)
Gene names: psbI, tsr1074
Sequence domains: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
Photosystem II reaction center protein J Chains: J, j
Molecule details ›
Chains: J, j
Length: 40 amino acids
Theoretical weight: 4.11 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: P59087 (Residues: 1-40; Coverage: 100%)
Gene names: psbJ, tsr1544
Sequence domains: PsbJ
Photosystem II reaction center protein K Chains: K, k
Molecule details ›
Chains: K, k
Length: 37 amino acids
Theoretical weight: 4.1 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q9F1K9 (Residues: 10-46; Coverage: 80%)
Gene names: psbK, tsl0176
Photosystem II reaction center protein L Chains: L, l
Molecule details ›
Chains: L, l
Length: 35 amino acids
Theoretical weight: 4.04 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DIN8 (Residues: 3-37; Coverage: 95%)
Gene names: psbL, tsr1543
Photosystem II manganese-stabilizing polypeptide Chains: O, o
Molecule details ›
Chains: O, o
Length: 243 amino acids
Theoretical weight: 26.52 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: P0A431 (Residues: 30-272; Coverage: 99%)
Gene names: psbO, tll0444
Structure domains:
Photosystem II reaction center protein T Chains: T, t
Molecule details ›
Chains: T, t
Length: 30 amino acids
Theoretical weight: 3.65 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DIQ0 (Residues: 1-30; Coverage: 94%)
Gene names: psbT, tsr1531
Sequence domains: Photosystem II reaction centre T protein
Photosystem II 12 kDa extrinsic protein Chains: U, u
Molecule details ›
Chains: U, u
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q9F1L5 (Residues: 38-134; Coverage: 93%)
Gene names: psbU, tll2409
Sequence domains: Photosystem II 12 kDa extrinsic protein (PsbU)
Structure domains: Photosystem II 12 kDa extrinsic protein
Cytochrome c-550 Chains: V, v
Molecule details ›
Chains: V, v
Length: 137 amino acids
Theoretical weight: 15.15 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: P0A386 (Residues: 27-163; Coverage: 100%)
Gene names: psbV, tll1285
Sequence domains: Cytochrome c-550 domain
Structure domains: Cytochrome c-like domain
Photosystem II reaction center protein Ycf12 Chains: Y, y
Molecule details ›
Chains: Y, y
Length: 29 amino acids
Theoretical weight: 3.1 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DJI1 (Residues: 18-46; Coverage: 63%)
Gene names: tsr1242, ycf12
Photosystem II reaction center X protein Chains: X, x
Molecule details ›
Chains: X, x
Length: 37 amino acids
Theoretical weight: 3.83 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q9F1R6 (Residues: 2-38; Coverage: 90%)
Gene names: psbX, tsr2013
Photosystem II reaction center protein Z Chains: Z, z
Molecule details ›
Chains: Z, z
Length: 62 amino acids
Theoretical weight: 6.77 KDa
Source organism: Thermosynechococcus elongatus BP-1
UniProt:
  • Canonical: Q8DHJ2 (Residues: 1-62; Coverage: 100%)
Gene names: psbZ, tsr1967
Sequence domains: YCF9
Structure domains: Photosystem II PsbZ, reaction centre

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 121.954Å b: 226.993Å c: 285.886Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.174 0.226