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- PDB-2vpl: The structure of the complex between the first domain of L1 prote... -

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Basic information

Entry
Database: PDB / ID: 2vpl
TitleThe structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii
Components
  • 50S RIBOSOMAL PROTEIN L1
  • FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
KeywordsTRANSLATION / RIBOSOMAL PROTEIN / RNA-PROTEIN COMPLEX / TRANSLATION REGULATION / REPRESSOR / RNA-BINDING / TRNA-BINDING / RRNA-BINDING
Function / homology
Function and homology information


regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
50S ribosomal protein L1; Chain A, Domain 1 / Arc Repressor Mutant, subunit A / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family ...50S ribosomal protein L1; Chain A, Domain 1 / Arc Repressor Mutant, subunit A / Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Helix non-globular / Special
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Large ribosomal subunit protein uL1
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
METHANOCALDOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKljashtorny, V. / Tishchenko, S. / Nevskaya, N. / Nikonov, S. / Garber, M.
CitationJournal: J. Mol. Biol. / Year: 2008
Title: Domain II of Thermus thermophilus ribosomal protein L1 hinders recognition of its mRNA.
Authors: Tishchenko, S. / Kljashtorny, V. / Kostareva, O. / Nevskaya, N. / Nikulin, A. / Gulak, P. / Piendl, W. / Garber, M. / Nikonov, S.
History
DepositionMar 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _pdbx_database_status.status_code_sf / _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.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.value / _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_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_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: 50S RIBOSOMAL PROTEIN L1
B: FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
C: 50S RIBOSOMAL PROTEIN L1
D: FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4666
Polymers61,3874
Non-polymers782
Water5,729318
1
A: 50S RIBOSOMAL PROTEIN L1
B: FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7333
Polymers30,6942
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-9 kcal/mol
Surface area17820 Å2
MethodPQS
2
C: 50S RIBOSOMAL PROTEIN L1
D: FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7333
Polymers30,6942
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-10 kcal/mol
Surface area17330 Å2
MethodPQS
Unit cell
Length a, b, c (Å)76.100, 144.350, 56.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-2074-

HOH

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L1


Mass: 15171.353 Da / Num. of mol.: 2 / Fragment: FIRST DOMAIN, RESIDUES 2-68,160-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P27150
#2: RNA chain FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE


Mass: 15522.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.44 Å3/Da / Density % sol: 49 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 26880 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.6 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HW8

2hw8


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1401 5 %RANDOM
Rwork0.209 ---
obs0.212 26514 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---3.42 Å20 Å2
3---4.05 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 2020 2 318 4480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214480
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4152.5256524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0215280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.88322.29296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86515395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.4591522
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022654
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.21528
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22780
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0680.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.1461.51383
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.92922240
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.36133097
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.4944.54279
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 98
Rwork0.267 1905

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