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- PDB-1c04: IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP O... -

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Basic information

Entry
Database: PDB / ID: 1c04
TitleIDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI
Components
  • (23S RRNA FRAGMENT) x 2
  • (RIBOSOMAL PROTEIN ...) x 4
KeywordsRIBOSOME / LOW RESOLUTION MODEL / LARGE RIBOSOME UNIT
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / 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 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L6, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 5 Å
AuthorsBan, N. / Nissen, P. / Capel, M. / Moore, P.B. / Steitz, T.A.
Citation
Journal: Nature / Year: 1999
Title: Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit.
Authors: Ban, N. / Nissen, P. / Hansen, J. / Capel, M. / Moore, P.B. / Steitz, T.A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: A 9 A resolution X-ray crystallographic map of the large ribosomal subunit
Authors: Ban, N. / Freeborn, B. / Nissen, P. / Penczec, P. / Grassucci, R.A. / Sweet, R. / Frank, J. / Moore, P.B. / Steitz, T.A.
History
DepositionJul 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 23S RRNA FRAGMENT
F: 23S RRNA FRAGMENT
A: RIBOSOMAL PROTEIN L2
B: RIBOSOMAL PROTEIN L6
C: RIBOSOMAL PROTEIN L11
D: RIBOSOMAL PROTEIN L14


Theoretical massNumber of molelcules
Total (without water)82,7216
Polymers82,7216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.000, 301.400, 576.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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RNA chain , 2 types, 2 molecules EF

#1: RNA chain 23S RRNA FRAGMENT


Mass: 18725.191 Da / Num. of mol.: 1 / Fragment: 23S RRNA 1151-1208 REGION / Source method: isolated from a natural source / Details: RNA E. COLI SEQUENCE AND MODEL / Source: (natural) Haloarcula marismortui (Halophile)
#2: RNA chain 23S RRNA FRAGMENT


Mass: 9376.676 Da / Num. of mol.: 1 / Fragment: 23S RRNA HELIX 95 / Source method: isolated from a natural source / Details: RNA RAT SEQUENCE AND MODEL / Source: (natural) Haloarcula marismortui (Halophile)

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RIBOSOMAL PROTEIN ... , 4 types, 4 molecules ABCD

#3: Protein RIBOSOMAL PROTEIN L2


Mass: 14930.819 Da / Num. of mol.: 1 / Fragment: CENTRAL RNA-BINDING DOMAINS / Source method: isolated from a natural source
Details: MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1RL2
Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P04257
#4: Protein RIBOSOMAL PROTEIN L6


Mass: 19202.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1RL6
Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P02391
#5: Protein RIBOSOMAL PROTEIN L11


Mass: 7116.356 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Source method: isolated from a natural source
Details: MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1QA6
Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P56210
#6: Protein RIBOSOMAL PROTEIN L14


Mass: 13369.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MODELED BY ANALOGOUS PROTEIN OF B. STEAROTHERMOPHILUS TAKEN FROM PDB ENTRY 1WHI
Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P04450

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Details

Has protein modificationY

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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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCL11
2NH4CL11
3MGCL211
4SODIUM ACETATE11
5PEG 600011
6PEG 600012
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 5.6 / Method: vapor diffusion / Details: von Bohlen, K., (1991) J. Mol. Biol., 222, 11.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
21.2 M1dropKCl
30.005 M1dropMgCl2
45-6 %PEG60001drop
50.1 Macetate1drop
60.00185 mM1dropCdCl2
70.0074 mMbeta-octylglucoside1drop
81.7 M1reservoirKCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X12B11.22
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 15, 1998
BRANDEIS - B42CCDJun 15, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.221
21.11
ReflectionResolution: 3.75→130 Å / Num. all: 185190 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 13
Reflection shellResolution: 3.75→3.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.513 / % possible all: 96
Reflection
*PLUS
Num. obs: 185190 / Num. measured all: 957850
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
CNSrefinement
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 5→60 Å / Num. reflection all: 77078 / Num. reflection obs: 76415 / σ(F): 2
Details: COMBINED MIRAS AND SAD PHASES WERE DETERMINED FROM ONE NATIVE AND FOUR DERIVATIVE CRYSTALS. PHASES WERE REFINED BY MULTI-CRYSTAL AVERAGING USING THREE CRYSTAL FORMS AND BY DENSITY ...Details: COMBINED MIRAS AND SAD PHASES WERE DETERMINED FROM ONE NATIVE AND FOUR DERIVATIVE CRYSTALS. PHASES WERE REFINED BY MULTI-CRYSTAL AVERAGING USING THREE CRYSTAL FORMS AND BY DENSITY MODIFICATION. RIBOSOMAL PROTEINS AND RNA FRAGMENTS WERE MANUALLY FITTED TO THE MAP CALCULATED AT 60 - 5 A RESOLUTION. NO COMPUTATIONAL REFINEMENT OF THE FITTING HAS BEEN PERFORMED. THE L6 DOMAINS HAVE BEEN MOVED RELATIVE TO EACH OTHER BY APPROXIMATELY 5 DEG. TO IMPROVE THE FIT TO DENSITY. THE L11-RNA COMPLEX HAS BEEN SLIGHTLY ADJUSTED TO OPTIMIZE THE FIT TO DENSITY OF BOTH L11 AND THE 58NT RRNA FRAGMENT SEPARATELY.
Refinement stepCycle: LAST / Resolution: 5→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 1864 0 0 5570
Refinement
*PLUS
Highest resolution: 5 Å / Lowest resolution: 60 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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