4V9O

Control of ribosomal subunit rotation by elongation factor G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.223

Literature

Macromolecules
Sequence Display for 4V9O

Classification: Ribosome / antibiotic

Total Structure Weight: 8946539.00


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 AC, CC, EC, GC 273 Escherichia coli Gene Name(s): rplB b3317 JW3279
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 AD, CD, ED, GD 209 Escherichia coli Gene Name(s): rplC b3320 JW3282
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 AE, CE, EE, GE 201 Escherichia coli Gene Name(s): rplD eryA b3319 JW3281
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 AF, CF, EF, GF 179 Escherichia coli Gene Name(s): rplE b3308 JW3270
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 AG, CG, EG, GG 177 Escherichia coli Gene Name(s): rplF b3305 JW3267
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 AH, CH, EH, GH 50 Escherichia coli Gene Name(s): rplI b4203 JW4161
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 AI, CI, EI, GI 142 Escherichia coli Gene Name(s): rplK relC b3983 JW3946
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 AJ, CJ, EJ, GJ 142 Escherichia coli Gene Name(s): rplM b3231 JW3200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 AK, CK, EK, GK 123 Escherichia coli Gene Name(s): rplN b3310 JW3272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 AL, CL, EL, GL 144 Escherichia coli Gene Name(s): rplO b3301 JW3263
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 AM, CM, EM, GM 136 Escherichia coli Gene Name(s): rplP b3313 JW3275
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 AN, CN, EN, GN 127 Escherichia coli Gene Name(s): rplQ b3294 JW3256
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 AO, CO, EO, GO 117 Escherichia coli Gene Name(s): rplR b3304 JW3266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 AP, CP, EP, GP 115 Escherichia coli Gene Name(s): rplS b2606 JW2587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 AQ, CQ, EQ, GQ 118 Escherichia coli Gene Name(s): rplT pdzA b1716 JW1706
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 AR, CR, ER, GR 103 Escherichia coli Gene Name(s): rplU b3186 JW3153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 AS, CS, ES, GS 110 Escherichia coli Gene Name(s): rplV eryB b3315 JW3277
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 AT, CT, ET, GT 100 Escherichia coli Gene Name(s): rplW b3318 JW3280
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 AU, CU, EU, GU 104 Escherichia coli Gene Name(s): rplX b3309 JW3271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 AV, CV, EV, GV 94 Escherichia coli Gene Name(s): rplY b2185 JW2173
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 AW, CW, EW, GW 85 Escherichia coli Gene Name(s): rpmA b3185 JW3152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 AX, CX, EX, GX 78 Escherichia coli Gene Name(s): rpmB b3637 JW3612
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 AY, CY, EY, GY 63 Escherichia coli Gene Name(s): rpmC b3312 JW3274
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 AZ, CZ, EZ, GZ 59 Escherichia coli Gene Name(s): rpmD b3302 JW3264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 A0, C0, E0, G0 57 Escherichia coli Gene Name(s): rpmF b1089 JW1075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 A1, C1, E1, G1 55 Escherichia coli Gene Name(s): rpmG b3636 JW3611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 A2, C2, E2, G2 46 Escherichia coli Gene Name(s): rpmH rimA ssaF b3703 JW3680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 A3, C3, E3, G3 65 Escherichia coli Gene Name(s): rpmI b1717 JW1707
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 A4, C4, E4, G4 38 Escherichia coli Gene Name(s): rpmJ b3299 JW3261
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10 A5, C5, E5 165 Escherichia coli Gene Name(s): rplJ b3985 JW3948
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7/L12 A6 121 Escherichia coli Gene Name(s): rplL b3986 JW3949
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 BB, DB, FB, HB 241 Escherichia coli Gene Name(s): rpsB b0169 JW0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 BC, DC, FC, HC 233 Escherichia coli Gene Name(s): rpsC b3314 JW3276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 BD, DD, FD, HD 206 Escherichia coli Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 BE, DE, FE, HE 167 Escherichia coli Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 BF, DF, FF, HF 135 Escherichia coli Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 BG, DG, FG, HG 179 Escherichia coli Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 BH, DH, FH, HH 130 Escherichia coli Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 BI, DI, FI, HI 130 Escherichia coli Gene Name(s): rpsI b3230 JW3199
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 BJ, DJ, FJ, HJ 103 Escherichia coli Gene Name(s): rpsJ nusE b3321 JW3283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 BK, DK, FK, HK 129 Escherichia coli Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 BL, DL, FL, HL 124 Escherichia coli Gene Name(s): rpsL strA b3342 JW3304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 BM, DM, FM, HM 118 Escherichia coli Gene Name(s): rpsM b3298 JW3260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 BN, DN, FN, HN 101 Escherichia coli Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 BO, DO, FO, HO 89 Escherichia coli Gene Name(s): rpsO secC b3165 JW3134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 BP, DP, FP, HP 82 Escherichia coli Gene Name(s): rpsP b2609 JW2590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 BQ, DQ, FQ, HQ 84 Escherichia coli Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 BR, DR, FR, HR 75 Escherichia coli Gene Name(s): rpsR b4202 JW4160
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 BS, DS, FS, HS 92 Escherichia coli Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 BT, DT, FT, HT 87 Escherichia coli Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S21 BU, DU, FU, HU 71 Escherichia coli Gene Name(s): rpsU b3065 JW3037
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Elongation factor G BV, DV, FV, HV 704 Escherichia coli Gene Name(s): fusA far fus b3340 JW3302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Viomycin BW, DW, FW, HW 6 Streptomyces
Macromolecule Entities
Molecule Chains Length Organism Details
5S rRNA AB, CB, EB, GB 120 Escherichia coli
23S rRNA AA, CA, EA, GA 2904 Escherichia coli
16S rRNA BA, DA, FA, HA 1542 Escherichia coli

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GCP
Query on GCP

BV, DV, FV, HV PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A4, C4, E4, G4 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A4, AA, AB, AC, AE, BA, BE, BN, BU, BV, C4, CA, CB, CE, CN, DA, DV, EA, EB, ED, EE, FA, FE, FN, FU, FV, GA, GB, GC, GL, HA, HE, HK, HV MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000226
Query on PRD_000226
BW, DW, FW, HW Viomycin Oligopeptide /
Antibiotic
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.223
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 361.60 α = 90.00
b = 361.77 β = 103.57
c = 433.20 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2013-05-03
  • Released Date: 2014-07-09
  • Deposition author(s): Pulk, A., Cate, J.H.D.
  • This entry supercedes: 4KIX 4KIY 4KIZ 4KJ0 4KJ1 4KJ2 4KJ3 4KJ4

Revision History

  • Version 1_0: 2014-07-09

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other

  • Version 1_2: 2014-12-17

    Type: Structure summary