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- PDB-1s03: The Structure of a Ribosomal Protein S8/spc Operon mRNA Complex -

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Basic information

Entry
Database: PDB / ID: 1s03
TitleThe Structure of a Ribosomal Protein S8/spc Operon mRNA Complex
Components
  • 30S ribosomal protein S8
  • 47-MER
KeywordsTRANSCRIPTION/RNA / protein-RNA complex / ribosomal / spc operon / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


regulation of mRNA stability / ribosomal small subunit assembly / cytosolic small ribosomal subunit / regulation of translation / cytoplasmic translation / rRNA binding / structural constituent of ribosome / cytosol / cytoplasm
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal Protein S8; Chain: A, domain 1 / Dna Ligase; domain 1 / : / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S8 signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS8
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMerianos, H.J. / Wang, J. / Moore, P.B.
CitationJournal: RNA / Year: 2004
Title: The structure of a ribosomal protein S8/spc operon mRNA complex.
Authors: Merianos, H.J. / Wang, J. / Moore, P.B.
History
DepositionDec 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 47-MER
B: 47-MER
H: 30S ribosomal protein S8
G: 30S ribosomal protein S8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,37521
Polymers58,2634
Non-polymers1,11217
Water905
1
A: 47-MER
H: 30S ribosomal protein S8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,72011
Polymers29,1312
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 47-MER
G: 30S ribosomal protein S8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,65510
Polymers29,1312
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.22, 61.22, 332.52
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21H
31G
41H
12A
22B
32A
42B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPVALVALGD4 - 504 - 50
211ASPASPVALVALHC4 - 504 - 50
321LEULEUALAALAGD58 - 12958 - 129
421LEULEUALAALAHC58 - 12958 - 129
112GGGGAA11 - 2111 - 21
212GGGGBB11 - 2111 - 21
322CCCCAA30 - 3930 - 39
422CCCCBB30 - 3930 - 39

NCS ensembles :
ID
1
2

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Components

#1: RNA chain 47-MER


Mass: 15116.042 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transciption, sequence from E. coli spc operon
#2: Protein 30S ribosomal protein S8 /


Mass: 14015.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7W7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 8000, zinc acetate, sodium acetate buffer, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2zinc acetate11
3sodium acetate buffer11
4H2O11
5PEG 80012
6zinc acetate12
7sodium acetate buffer12
8H2O12

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.0049
SYNCHROTRONNSLS X2520.9928
SYNCHROTRONNSLS X2531.008998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00491
20.99281
31.0089981
ReflectionResolution: 2.7→50 Å / Num. obs: 20950
Reflection shellResolution: 2.7→2.8 Å / Num. unique all: 3907

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J5E

1j5e


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.192 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.642 / ESU R Free: 0.335
RfactorNum. reflection% reflectionSelection details
Rfree0.27313 1070 5.1 %RANDOM
Rwork0.23734 ---
all0.23917 ---
obs0.23734 19880 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 2008 17 5 3951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214185
X-RAY DIFFRACTIONr_angle_refined_deg2.3312.576102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9055251
X-RAY DIFFRACTIONr_chiral_restr0.1030.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022374
X-RAY DIFFRACTIONr_nbd_refined0.2340.21638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.27
X-RAY DIFFRACTIONr_mcbond_it2.1873.51253
X-RAY DIFFRACTIONr_mcangle_it3.77342010
X-RAY DIFFRACTIONr_scbond_it3.79852932
X-RAY DIFFRACTIONr_scangle_it5.82584092
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1G903tight positional0.060.05
2A449tight positional0.10.05
1G903tight thermal0.190.5
2A449tight thermal0.250.5
LS refinement shellResolution: 2.7→2.846 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.451 155
Rwork0.421 2819
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.7711-1.62950.21849.26822.41295.3678-0.1844-0.5781.05670.12510.166-1.4775-0.3135-0.19480.01840.30620.16950.03160.1716-0.12350.725337.857716.3348116.555
25.0988-2.3433.22933.0517-0.53383.49160.43190.4751-0.0941-0.2652-0.40590.16820.37050.5858-0.0260.32560.04280.02370.17160.03150.301925.263531.0949.9943
34.97980.2285-0.86663.90570.24457.54090.6335-0.37550.60570.4184-0.2330.4303-0.4759-0.3686-0.40050.2751-0.05030.19770.0102-0.02340.30318.927440.272763.3524
40.90350.0880.33352.6727-1.76353.2937-0.0998-0.1184-0.10730.05120.1195-0.20130.1852-0.079-0.01980.46850.15360.13920.27940.0090.352337.724-3.1373104.6358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1GD4 - 1294 - 129
2X-RAY DIFFRACTION2AA1 - 471 - 47
3X-RAY DIFFRACTION3HC4 - 1294 - 129
4X-RAY DIFFRACTION4BB1 - 471 - 47

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