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- PDB-1hc8: CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1hc8
TitleCRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX
Components
  • 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
  • RIBOSOMAL PROTEIN L11
KeywordsRIBOSOME / RIBOSOMAL RNA / TERTIARY STRUCTURE / RNA-PROTEIN
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA binding
Similarity search - Function
Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily ...Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / OSMIUM ION / RNA / RNA (> 10) / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsConn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: A Compact RNA Tertiary Structure Contains a Buried Backbone-K+ Complex
Authors: Conn, G.L. / Gittis, A.G. / Lattman, E.E. / Misra, V.K. / Draper, D.E.
#1: Journal: Science / Year: 1999
Title: Crystal Structure of a Conserved Ribosomal Protein-RNA Complex
Authors: Conn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
History
DepositionApr 27, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L11
B: RIBOSOMAL PROTEIN L11
C: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
D: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,45531
Polymers54,1054
Non-polymers1,35027
Water23413
1
A: RIBOSOMAL PROTEIN L11
C: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,71515
Polymers27,0532
Non-polymers66313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RIBOSOMAL PROTEIN L11
D: 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,74016
Polymers27,0532
Non-polymers68714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.675, 150.675, 63.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.043157, -0.998994, -0.012207), (-0.392208, -0.005704, -0.919859), (0.918863, 0.044486, -0.39206)
Vector: 166.83, 180.4792, -58.8074)
DetailsCOMPLEX OF THE RIBOSOMAL PROTEIN L11 AND THERIBOSOMAL 23S RNA FRAGMENT

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein RIBOSOMAL PROTEIN L11 /


Mass: 8167.547 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PET11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56210
#2: RNA chain 58 NUCLEOTIDE RIBOSOMAL 23S RNA DOMAIN


Mass: 18885.150 Da / Num. of mol.: 2 / Fragment: NTS 1051-1108 FROM E. COLI 23S RRNA / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: RNA SYNTHESIZED BY IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE
Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 4 types, 40 molecules

#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-OS / OSMIUM ION / Osmium


Mass: 190.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Os
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN C, D ENGINEERED MUTATION U1601A

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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: 3.35 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.5
Details: PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop / Details: Conn, G.L., (1999) Science, 284, 1171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium cacodylate1reservoir
215 %PEG6001reservoir
380 mM1reservoirMg(OAc)2
4100 mM1reservoirKCl
50.2 mM1reservoirCo(NH3)6Cl3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.13951
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13951 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 17542 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.24 / Net I/σ(I): 5.9
Reflection shellResolution: 2.8→2.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.27 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. measured all: 89078 / Rmerge(I) obs: 0.55
Reflection shell
*PLUS
% possible obs: 88.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.9

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1373 7.8 %RANDOM
Rwork0.217 ---
obs0.217 17542 94.5 %-
Solvent computationSolvent model: CNS
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 2504 27 13 3607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.03
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 27
RfactorNum. reflection% reflection
Rfree0.425 48 7.8 %
Rwork0.368 525 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
LS refinement shell
*PLUS
Rfactor obs: 0.368

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