ISDA

Deposition Date 2013-12-09

Release Date 2014-05-21

Last Version Date 2025-02-19

Entry Detail

PDB ID:

4NXM

Keywords:

RIBOSOME

Title:

Crystal Structure of the 30S ribosomal subunit from a GidB (RsmG) mutant of Thermus thermophilus (HB8)

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 300852)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.65 Å

R-Value Free:

0.22

R-Value Work:

0.17

R-Value Observed:

0.18

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S8
Chain IDs:H
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:135
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:F6DEQ7 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S14
Chain IDs:N
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S17
Chain IDs:Q
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ribosomal protein THX
Gene (Uniprot):rpsU
Chain IDs:U
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
0TD	L	ASP	(3S)-3-(METHYLSULFANYL)-L-ASPARTIC ACID
2MG	A	G	2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
4OC	A	C	4N,O2'-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MC	A	C	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
M2G	A	G	N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
MA6	A	A	6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE
PSU	A	U	PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3	A	U	3-METHYLURIDINE-5'-MONOPHOSHATE