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- PDB-1feu: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TL5, ONE OF THE CTC FAMILY... -

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Basic information

Entry
Database: PDB / ID: 1feu
TitleCRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN TL5, ONE OF THE CTC FAMILY PROTEINS, COMPLEXED WITH A FRAGMENT OF 5S RRNA.
Components
  • 19 NT FRAGMENT OF 5S RRNA
  • 21 NT FRAGMENT OF 5S RRNA
  • 50S RIBOSOMAL PROTEIN L25
KeywordsRIBOSOME / general stress protein CTC / 5S rRNA-protein complex / cadmium ions
Function / homology
Function and homology information


5S rRNA binding / ribosome / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L25, C-terminal domain / Ribosomal Protein L25; Chain P / Ribosomal Protein L25; Chain P / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal L25p family / Ribosomal protein L25 ...Ribosomal protein L25, C-terminal domain / Ribosomal Protein L25; Chain P / Ribosomal Protein L25; Chain P / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal L25p family / Ribosomal protein L25 / Beta Complex / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / 50S ribosomal protein L25
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsFedorov, R.V. / Meshcheryakov, V.A. / Gongadze, G.M. / Fomenkova, N.P. / Nevskaya, N.A. / Selmer, M. / Laurberg, M. / Kristensen, O. / Al-Karadaghi, S. / Liljas, A. ...Fedorov, R.V. / Meshcheryakov, V.A. / Gongadze, G.M. / Fomenkova, N.P. / Nevskaya, N.A. / Selmer, M. / Laurberg, M. / Kristensen, O. / Al-Karadaghi, S. / Liljas, A. / Garber, M.B. / Nikonov, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins.
Authors: Fedorov, R. / Meshcheryakov, V. / Gongadze, G. / Fomenkova, N. / Nevskaya, N. / Selmer, M. / Laurberg, M. / Kristensen, O. / Al-Karadaghi, S. / Liljas, A. / Garber, M. / Nikonov, S.
History
DepositionJul 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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
B: 19 NT FRAGMENT OF 5S RRNA
C: 21 NT FRAGMENT OF 5S RRNA
E: 19 NT FRAGMENT OF 5S RRNA
F: 21 NT FRAGMENT OF 5S RRNA
A: 50S RIBOSOMAL PROTEIN L25
D: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,37336
Polymers72,4996
Non-polymers1,87530
Water5,314295
1
B: 19 NT FRAGMENT OF 5S RRNA
C: 21 NT FRAGMENT OF 5S RRNA
A: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,07015
Polymers36,2493
Non-polymers82012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 19 NT FRAGMENT OF 5S RRNA
F: 21 NT FRAGMENT OF 5S RRNA
D: 50S RIBOSOMAL PROTEIN L25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,30421
Polymers36,2493
Non-polymers1,05418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.904, 109.904, 137.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Cell settingtrigonal
Space group name H-MP3112

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Components

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RNA chain , 2 types, 4 molecules BECF

#1: RNA chain 19 NT FRAGMENT OF 5S RRNA


Mass: 6206.706 Da / Num. of mol.: 2 / Fragment: INCLUDES LOOP E AND HELIX IV / Source method: obtained synthetically
#2: RNA chain 21 NT FRAGMENT OF 5S RRNA


Mass: 6790.141 Da / Num. of mol.: 2 / Fragment: INCLUDES LOOP E AND HELIX IV / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AD

#3: Protein 50S RIBOSOMAL PROTEIN L25 / / RIBOSOMAL PROTEIN TL5


Mass: 23252.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Description: BACTERIA / Production host: Escherichia coli (E. coli) / References: UniProt: P56930

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Non-polymers , 3 types, 325 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12-4 mg/mlprotein1drop
210 mMsodium cacodylate1drop
3100 mM1dropMgCl2
44 mM1dropCdCl2
57 %MPD1drop
6200 mM1reservoirKCl
712 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONMAX II I71111.108
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9794
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMay 1, 1999
MARRESEARCH2IMAGE PLATENov 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1081
20.97941
ReflectionResolution: 2.3→20 Å / Num. all: 41886 / Num. obs: 41886 / % possible obs: 98.8 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 44.14 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.365 / Num. unique all: 2067 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 188440
Reflection shell
*PLUS
% possible obs: 97.8 % / Mean I/σ(I) obs: 4.5

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Processing

Software
NameClassification
DMmodel building
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
DMphasing
RefinementResolution: 2.3→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3722 10 %random
Rwork0.208 ---
all-40543 --
obs-37059 91.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 1722 30 295 5025
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.1819
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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