1eg0
FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME
Method: ELECTRON MICROSCOPY
Dmax: 218.0 Å
Quality: REASONABLE
SAXS Profile
P(r) Distribution
▼
1. Structure Basics
| entry_id | 1eg0 |
| deposition_date | 2000-02-11 |
| title | FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME |
| keywords | 70S RIBOSOME, LOW RESOLUTION MODEL, RIBOSOME; RIBOSOME |
| method | ELECTRON MICROSCOPY |
▼
Download Data
▼
2. SAXS Parameters (CRYSOL)
| rg_guinier | 83.82 Å |
| rg_electron | 84.88 Å |
| i0 | 469794000.00 |
| molecular_weight | 169480.0 kDa |
| excluded_volume | 211570 ų |
| envelope_volume | 453860 ų |
| shell_volume | 50981 ų |
| envelope_diameter | 226.2 Å |
| shell_rg | 76.13 Å |
| envelope_rg | 71.34 Å |
| shape_rg | 84.14 Å |
| total_rg | 84.75 Å |
| total_atoms | 192 |
| n_residues | 187 |
| n_harmonics | 20 |
| q_range | — – 0.5000 Å−1 |
| n_points | 101 |
| shell_type | directional |
| solvent_density | 0.3340 e/ų |
| contrast_shell | 0.0300 e/ų |
| crysol_version | 4.1.3 |
▼
3. P(r) Analysis (GNOM)
| dmax | 218.0 Å |
| rg_real | 83.52 Å |
| rg_real_error | 1.30 Å |
| i0_real | 4.6980e+08 |
| i0_real_error | 1.0520e+07 |
| rg_reciprocal | 84.22 Å |
| i0_reciprocal | 470300000.0000 |
| total_estimate | 0.6060 |
| solution_quality | REASONABLE a REASONABLE solution |
| n_peaks | 1 |
| r_peak_primary | 137.7 Å |
| skewness | -0.171 |
| kurtosis | -0.899 |
| angular_range | — – 0.0950 Å−1 |
| current_alpha | 0.0007 |
| highest_alpha | 25320000.0000 |
| n_real_points | 20 |
| gnom_version | 4.1.3 |
| quality_criteria | AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 0.008; Positv: 1.000; Valcen: 0.929; Smooth: 0.000 |
▶
4. Crystallography & Experiment
Unit Cell
| length_a | 1.000 Å |
| length_b | 1.000 Å |
| length_c | 1.000 Å |
| angle_alpha | 90.00 ° |
| angle_beta | 90.00 ° |
| angle_gamma | 90.00 ° |
| z_pdb | 1 |
Symmetry
| space_group | P 1 |
| int_tables_number | 1 |
| crystal_system | — |
Refinement
| resolution | 11.500 Å |
| resolution_low | — Å |
| r_factor | — |
| r_work | — |
| r_free | — |
EM 3D
| resolution | 11.50 Å |
| resolution_method | — |
| num_particles | 73523 |
▶
5. Entities & Polymer Info (15)
Entity 1 polymer
| description | FRAGMENT OF 16S RRNA HELIX 23 |
| formula_weight | 6426.2 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polyribonucleotide |
| strand_id | I |
| atom_count | 1658 |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Entity 2 polymer
| description | FRAGMENT OF 23S RRNA |
| formula_weight | 18347.9 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polyribonucleotide |
| strand_id | L |
CUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
Entity 3 polymer
| description | HELIX 95 OF 23S RRNA |
| formula_weight | 8438.1 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polyribonucleotide |
| strand_id | M |
GCUCCUAGUACGAGAGGACCGGAGUG
Entity 4 polymer
| description | FORMYL-METHIONYL-TRNA |
| formula_weight | 24526.8 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polyribonucleotide |
| strand_id | O |
CGCGGGGUGGAGCAGCCGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA
Entity 5 polymer
| description | PROTEIN (S4 RIBOSOMAL PROTEIN) |
| formula_weight | 18624.4 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | A |
MKLSEYGLQLQEKQKLRHMYGVNERQFRKTFEEAGKMPGKHGENFMILLESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPGQTIAVREKSRNLQVIKEALEANNYIPDYLSFDPEKMEGTYTRLPERSELPAEINEALIVEFYSR
Entity 6 polymer
| description | PROTEIN (S5 RIBOSOMAL PROTEIN) |
| formula_weight | 15686.3 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | B |
MRRINPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRATFDGLKQLK
Entity 7 polymer
| description | PROTEIN (S6 RIBOSOMAL PROTEIN) |
| formula_weight | 11619.3 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | C |
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPF
Entity 8 polymer
| description | PROTEIN (S7 RIBOSOMAL PROTEIN) |
| formula_weight | 16758.5 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | D |
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKVFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIAHELMDAAEGKGGAVKKKEDVERMAE
Entity 9 polymer
| description | PROTEIN (S8 RIBOSOMAL PROTEIN) |
| formula_weight | 15868.6 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | E |
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREARKLGVGGELICEVW
Entity 10 polymer
| description | PROTEIN (S15 RIBOSOMAL PROTEIN) |
| formula_weight | 10578.4 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | F |
MPITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVGQRRRLLRYLQREDPERYRALIEKLGIRG
Entity 11 polymer
| description | PROTEIN (S17 RIBOSOMAL PROTEIN) |
| formula_weight | 10569.3 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | G |
SERNQRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVEKAVRAGAGAGAA
Entity 12 polymer
| description | PROTEIN (S20 RIBOSOMAL PROTEIN) |
| formula_weight | 8528.5 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | H |
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Entity 13 polymer
| description | PROTEIN (RIBOSOMAL PROTEIN L1) |
| formula_weight | 24867.7 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | N |
MPKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS
Entity 14 polymer
| description | PROTEIN (RIBOSOMAL PROTEIN L6) |
| formula_weight | 18601.5 kDa |
| mutation | B. STEAROTHERMOPHILUS SEQUENCE AND MODEL |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | J |
MSRVGKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRALHGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKGKGIRYEGELVRL
Entity 15 polymer
| description | PROTEIN (RIBOSOMAL PROTEIN L11) |
| formula_weight | 14996.8 kDa |
| src_method | nat |
| entity_count | 1 |
Polymer
| type | polypeptide(L) |
| strand_id | K |
MAKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVV
▶
6. Citations (14)
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
Cell(Cambridge,Mass.) (2000)
A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
Cell(Cambridge,Mass.) (1999)
The Two Faces of the Escherichia Coli 23 S Rrna Sarcin/Ricin Domain: The Structure at 1.11 A Resolution
J.Mol.Biol. (1999)
Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution
Nature (1999)
;The Crystal Structure of Ribosomal Protein S4 Reveals a Two-Domain Molecule with an Extensive RNA-Binding Surface: One Domain Shows Structural Homology to the Ets DNA-Binding Motif
;
Embo J. (1998)
Crystal Structure of Methionyl-Trnafmet Transformylase Complexed with the Initiator Formyl-Methionyl-Trnafmet
Embo J. (1998)
;Crystal Structure of Ribosomal Protein S8 from Thermus Thermophilus Reveals a High Degree of Structural Conservation of a Specific RNA Binding Site
;
J.Mol.Biol. (1998)
Conformational Variability of the N-Terminal Helix in the Structure of Ribosomal Protein S15
Structure (1998)
The Structure of Ribosomal Protein S7 at 1.9 A Resolution Reveals a Beta- Hairpin Motif that Binds Double-Stranded Nucleic Acids
Structure (1997)
Crystal Structure of the RNA Binding Ribosomal Prot L1 from Thermus Thermophilus
Embo J. (1996)
Solution Structure of Prokaryotic Ribosomal Protein S17 by High-Resolution NMR Spectroscopy
Biochemistry (1996)
DOI: 10.1021/bi951062i
Crystal Structure of the Ribosomal Protein S6 from Thermus Thermophilus
Embo J. (1994)
Ribosomal Protein L6: Structural Evidence of Gene Duplication from a Primitive RNA-Binding Protein
Embo J. (1993)
The Structure of Ribosomal Protein S5 Reveals Sites of Interaction with 16S Rrna
Nature (1992)
DOI: 10.1038/358768a0
▶
7. Files & Curves (10)
Files (7)
- pr_distribution /app/data/pr_computation/eg/1eg0/pr_distribution.json
- pr_output /app/data/pr_computation/eg/1eg0/1eg0.pr.out
- pr_plot /app/data/visualization/pr_computation/eg/1eg0/1eg0_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/eg/1eg0/1eg0.dat
- saxs_fit /app/data/saxs_computation/eg/1eg0/1eg0.fit
- saxs_log /app/data/saxs_computation/eg/1eg0/1eg0.log
- saxs_plot /app/data/visualization/saxs_computation/eg/1eg0/1eg0_saxs_profile.png
Curves (3)
| fit | /app/data/saxs_computation/eg/1eg0/1eg0.fit |
| pddf | /app/data/pr_computation/eg/1eg0/1eg0.pr.out |
| profile | /app/data/saxs_computation/eg/1eg0/1eg0.dat |