› 4kvb

X-ray diffraction
4.2Å resolution

Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17

Released:
DOI: 10.2210/pdb4kvb/pdb
PDB entry 4kvb coloured by chain, front view.
PDB entry 4kvb coloured by chain, side view.
PDB entry 4kvb coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Entry authors: Murphy EL, Jogl G

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215997 (preferred)
Entry contents:
19 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (20 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 1-256; Coverage: 100%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 1-239; Coverage: 100%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62664 (Residues: 1-209; Coverage: 100%)
Gene names: TT_C1301, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: E
Molecule details ›
Chain: E
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62665 (Residues: 1-162; Coverage: 100%)
Gene names: TT_C1311, rps5, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: F
Molecule details ›
Chain: F
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62666 (Residues: 1-101; Coverage: 100%)
Gene names: TT_C1740, rps6, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: G
Molecule details ›
Chain: G
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62667 (Residues: 1-156; Coverage: 100%)
Gene names: TT_C1332, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: H
Molecule details ›
Chain: H
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62668 (Residues: 1-138; Coverage: 100%)
Gene names: TT_C1314, rps8, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: I
Molecule details ›
Chain: I
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62669 (Residues: 1-128; Coverage: 100%)
Gene names: TT_C1100, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: J
Molecule details ›
Chain: J
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 1-105; Coverage: 100%)
Gene names: TT_C1329, rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: K
Molecule details ›
Chain: K
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 1-129; Coverage: 100%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: L
Molecule details ›
Chain: L
Length: 134 amino acids
Theoretical weight: 14.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 2-132; Coverage: 99%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: M
Molecule details ›
Chain: M
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 1-126; Coverage: 100%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: N
Molecule details ›
Chain: N
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62656 (Residues: 1-61; Coverage: 100%)
Gene names: TT_C1315, rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: O
Molecule details ›
Chain: O
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62657 (Residues: 1-89; Coverage: 100%)
Gene names: TT_C0773, rps15, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: P
Molecule details ›
Chain: P
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62238 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein bS18 Chain: R
Molecule details ›
Chain: R
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62659 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: S
Molecule details ›
Chain: S
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 1-93; Coverage: 100%)
Gene names: TT_C1324, rps19, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: T
Molecule details ›
Chain: T
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62661 (Residues: 1-106; Coverage: 100%)
Gene names: TT_C1031, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chain: U
Molecule details ›
Chain: U
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62613 (Residues: 1-27; Coverage: 100%)
Gene names: TT_C1030, rpsU
Sequence domains: 30S ribosomal protein Thx
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1522 nucleotides
Theoretical weight: 494.21 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 158 x MG
Ligand K 35 x K
Ligand ZN 2 x ZN
9 modified residues:
Ligand PSU 3 x PSU
Ligand 7MG 1 x 7MG
Ligand M2G 1 x M2G
Ligand 5MC 4 x 5MC
Ligand 2MG 1 x 2MG
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand 0TD 1 x 0TD

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P41212
Unit cell:
a: 397.316Å b: 397.316Å c: 215.505Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.217 0.258

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