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- PDB-4v4a: Crystal Structure of the Wild Type Ribosome from E. Coli 70S Ribosome. -

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Basic information

Entry
Database: PDB / ID: 4v4a
TitleCrystal Structure of the Wild Type Ribosome from E. Coli 70S Ribosome.
Components
  • (30S ribosomal protein ...) x 19
  • (50S ribosomal protein ...) x 30
  • 16S RIBOSOMAL RNA
  • 23S RIBOSOMAL RNA
  • 5S RIBOSOMAL RNA
  • general stress protein Ctc
KeywordsRIBOSOME / 30S RIBOSOMAL SUBUNIT / PROTEIN-PROTEIN COMPLEX / PROTEIN-RNA COMPLEX / RNA-RNA COMPLEX
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 9.5 Å
AuthorsVila-Sanjurjo, A. / Ridgeway, W.K. / Seymaner, V. / Zhang, W. / Santoso, S. / Yu, K. / Cate, J.H.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli
Authors: Vila-Sanjurjo, A. / Ridgeway, W.K. / Seymaner, V. / Zhang, W. / Santoso, S. / Yu, K. / Cate, J.H.D.
History
DepositionJun 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1PNX, 1PNY
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 400COMPOUND PDB ENTRIES 1PNX AND 1PNY REPRESENT ONE CRYSTAL STRUCTURE OF THE E. COLI 70S RIBOSOME. ...COMPOUND PDB ENTRIES 1PNX AND 1PNY REPRESENT ONE CRYSTAL STRUCTURE OF THE E. COLI 70S RIBOSOME. THIS FILE, 1PNX, CONTAINS ONLY MOLECULES OF THE 30S RIBOSOMAL SUBUNIT. THE 50S SUBUNIT IS IN THE PDB FILE 1PNY.
Remark 999SEQUENCE The 30S subunit is derived mainly from 1J5E, the T. thermophilus 30S subunit, with ...SEQUENCE The 30S subunit is derived mainly from 1J5E, the T. thermophilus 30S subunit, with modifications to the rRNA to make it match E. coli insertions and deletions. The sequence of this subunit represent that of pdb entry, 1J5E. As a result, no dbref was provided.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 16S RIBOSOMAL RNA
AB: 30S ribosomal protein S2
AC: 30S ribosomal protein S3
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S5
AF: 30S ribosomal protein S6
AG: 30S ribosomal protein S7
AH: 30S ribosomal protein S8
AI: 30S ribosomal protein S9
AJ: 30S ribosomal protein S10
AK: 30S ribosomal protein S11
AL: 30S ribosomal protein S12
AM: 30S ribosomal protein S13
AN: 30S ribosomal protein S14
AO: 30S ribosomal protein S15
AP: 30S ribosomal protein S16
AQ: 30S ribosomal protein S17
AR: 30S ribosomal protein S18
AS: 30S ribosomal protein S19
AT: 30S ribosomal protein S20
B0: 23S RIBOSOMAL RNA
B9: 5S RIBOSOMAL RNA
BA: 50S ribosomal protein L2
BB: 50S ribosomal protein L3
BC: 50S ribosomal protein L4
BD: 50S ribosomal protein L5
BE: 50S ribosomal protein L6
BF: 50S ribosomal protein L9
BG: 50S ribosomal protein L11
BH: 50S ribosomal protein L13
BI: 50S ribosomal protein L14
BJ: 50S ribosomal protein L15
BK: 50S ribosomal protein L16
BL: 50S ribosomal protein L17
BM: 50S ribosomal protein L18
BN: 50S ribosomal protein L19
BO: 50S ribosomal protein L20
BP: 50S ribosomal protein L21
BQ: 50S ribosomal protein L22
BR: 50S ribosomal protein L23
BS: 50S ribosomal protein L24
BT: general stress protein Ctc
BU: 50S ribosomal protein L27
BV: 50S RIBOSOMAL PROTEIN L28
BW: 50S ribosomal protein L29
BX: 50S ribosomal protein L30
BY: 50S ribosomal protein L31
BZ: 50S ribosomal protein L32
B1: 50S ribosomal protein L33
B2: 50S ribosomal protein L34
B3: 50S ribosomal protein L35
B4: 50S ribosomal protein L36
B5: 50S ribosomal protein L1P


Theoretical massNumber of molelcules
Total (without water)2,141,52353
Polymers2,141,52353
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)683.89, 683.89, 386.72
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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Components

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RNA chain , 3 types, 3 molecules AAB0B9

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 498797.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#21: RNA chain 23S RIBOSOMAL RNA /


Mass: 935779.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#22: RNA chain 5S RIBOSOMAL RNA /


Mass: 38029.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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30S ribosomal protein ... , 19 types, 19 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASAT

#2: Protein 30S ribosomal protein S2 /


Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: Protein 30S ribosomal protein S3 /


Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#4: Protein 30S ribosomal protein S4 /


Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#5: Protein 30S ribosomal protein S5 /


Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#6: Protein 30S ribosomal protein S6 / / TS9


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#7: Protein 30S ribosomal protein S7 /


Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#8: Protein 30S ribosomal protein S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#9: Protein 30S ribosomal protein S9 /


Mass: 14298.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#10: Protein 30S ribosomal protein S10 /


Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#11: Protein 30S ribosomal protein S11 /


Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#12: Protein 30S ribosomal protein S12 /


Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#13: Protein 30S ribosomal protein S13 /


Mass: 14207.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#14: Protein 30S ribosomal protein S14 /


Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#15: Protein 30S ribosomal protein S15 /


Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#16: Protein 30S ribosomal protein S16 /


Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#17: Protein 30S ribosomal protein S17 /


Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#18: Protein 30S ribosomal protein S18 /


Mass: 8483.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#19: Protein 30S ribosomal protein S19 /


Mass: 9203.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#20: Protein 30S ribosomal protein S20 /


Mass: 10907.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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50S ribosomal protein ... , 30 types, 30 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBUBVBWBXBYBZB1B2B3B4B5

#23: Protein 50S ribosomal protein L2 / / Coordinate model: Cα atoms only


Mass: 29519.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#24: Protein 50S ribosomal protein L3 / / Coordinate model: Cα atoms only


Mass: 21962.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#25: Protein 50S ribosomal protein L4 / / Coordinate model: Cα atoms only


Mass: 21405.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#26: Protein 50S ribosomal protein L5 / / Coordinate model: Cα atoms only


Mass: 20120.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#27: Protein 50S ribosomal protein L6 / / Coordinate model: Cα atoms only


Mass: 18680.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#28: Protein 50S ribosomal protein L9 / / Coordinate model: Cα atoms only


Mass: 5734.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#29: Protein 50S ribosomal protein L11 / / Coordinate model: Cα atoms only


Mass: 14818.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#30: Protein 50S ribosomal protein L13 / / Coordinate model: Cα atoms only


Mass: 15936.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#31: Protein 50S ribosomal protein L14 / / Coordinate model: Cα atoms only


Mass: 14012.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#32: Protein 50S ribosomal protein L15 / / Coordinate model: Cα atoms only


Mass: 15177.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#33: Protein 50S ribosomal protein L16 / / Coordinate model: Cα atoms only


Mass: 14033.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#34: Protein 50S ribosomal protein L17 / / Coordinate model: Cα atoms only


Mass: 12637.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#35: Protein 50S ribosomal protein L18 / / Coordinate model: Cα atoms only


Mass: 11860.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#36: Protein 50S ribosomal protein L19 / / Coordinate model: Cα atoms only


Mass: 14322.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#37: Protein 50S ribosomal protein L20 / / Coordinate model: Cα atoms only


Mass: 13860.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#38: Protein 50S ribosomal protein L21 / / Coordinate model: Cα atoms only


Mass: 11165.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#39: Protein 50S ribosomal protein L22 / / Coordinate model: Cα atoms only


Mass: 14790.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#40: Protein 50S ribosomal protein L23 / / Coordinate model: Cα atoms only


Mass: 10336.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#41: Protein 50S ribosomal protein L24 / / Coordinate model: Cα atoms only


Mass: 12138.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#43: Protein 50S ribosomal protein L27 / / Coordinate model: Cα atoms only


Mass: 9121.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#44: Protein/peptide 50S RIBOSOMAL PROTEIN L28 / / Coordinate model: Cα atoms only


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#45: Protein 50S ribosomal protein L29 / / Coordinate model: Cα atoms only


Mass: 7515.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#46: Protein 50S ribosomal protein L30 / / Coordinate model: Cα atoms only


Mass: 6079.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#47: Protein 50S ribosomal protein L31 / / Coordinate model: Cα atoms only


Mass: 8597.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#48: Protein 50S ribosomal protein L32 / / Coordinate model: Cα atoms only


Mass: 6579.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#49: Protein 50S ribosomal protein L33 / / Coordinate model: Cα atoms only


Mass: 6144.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#50: Protein/peptide 50S ribosomal protein L34 / / Coordinate model: Cα atoms only


Mass: 5497.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#51: Protein 50S ribosomal protein L35 / / Coordinate model: Cα atoms only


Mass: 7130.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#52: Protein/peptide 50S ribosomal protein L36 / / Coordinate model: Cα atoms only


Mass: 4134.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#53: Protein 50S ribosomal protein L1P / Ribosome / Coordinate model: Cα atoms only


Mass: 24690.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Protein , 1 types, 1 molecules BT

#42: Protein general stress protein Ctc / Coordinate model: Cα atoms only


Mass: 18929.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 5.28 Å3/Da / Density % sol: 76.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: MPD, ethanol, magnesium chloride, ammonium chloride, spermine, spermidine, MES , pH 6.5, VAPOR DIFFUSION, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2ethanol11
3magnesium chloride11
4ammonium chloride11
5spermine11
6spermidine11
7MES11
8H2O11
9MPD12
10magnesium chloride12
11ammonium chloride12
12H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0, 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2000
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.11
ReflectionResolution: 9.5→300 Å / Num. all: 29028 / Num. obs: 26821 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.1 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 44.8
Reflection shellResolution: 9.5→9.68 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.5 / % possible all: 71.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J5E,1LNR

1j5e

1lnr
PDB Unreleased entry


Resolution: 9.5→70 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: NA
Details: 87 RIGID-BODIES REFINEMENT, GROUPED B-FACTOR REFINEMENT. There are many long O3'-P distances. Coordinates used for solving and refining this structure mainly comes from PDB entry, 1J5E, ...Details: 87 RIGID-BODIES REFINEMENT, GROUPED B-FACTOR REFINEMENT. There are many long O3'-P distances. Coordinates used for solving and refining this structure mainly comes from PDB entry, 1J5E, where the sequence represents that of T. thermophilus.
RfactorNum. reflection% reflectionSelection details
Rfree0.407 1215 -RANDOM
Rwork0.389 ---
all-29028 --
obs-26821 92.1 %-
Displacement parametersBiso mean: 696.1 Å2
Refinement stepCycle: LAST / Resolution: 9.5→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19012 32939 0 0 51951

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