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- PDB-4bw0: The molecular recognition of kink turn structure by the L7Ae clas... -

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Basic information

Entry
Database: PDB / ID: 4bw0
TitleThe molecular recognition of kink turn structure by the L7Ae class of proteins
Components
  • 50S RIBOSOMAL PROTEIN L7AE
  • HMKT-7
KeywordsRNA/RNA BINDING PROTEIN / RNA-RNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
HALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: RNA / Year: 2013
Title: The Molecular Recognition of Kink-Turn Structure by the L7Ae Class of Proteins.
Authors: Huang, L. / Lilley, D.M.J.
History
DepositionJun 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 20, 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 / 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 / _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: HMKT-7
B: 50S RIBOSOMAL PROTEIN L7AE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1653
Polymers22,0692
Non-polymers961
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-18.4 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.920, 61.920, 130.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

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Components

#1: RNA chain HMKT-7


Mass: 8546.251 Da / Num. of mol.: 1 / Fragment: KINK TURN MOTIF, RESIDUES 1-26 / Source method: obtained synthetically / Source: (synth.) HALOARCULA MARISMORTUI (Halophile)
#2: Protein 50S RIBOSOMAL PROTEIN L7AE / L7AE


Mass: 13522.559 Da / Num. of mol.: 1 / Fragment: K-TURN BINDING DOMAIN, RESIDUES 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: O29494
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.78 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7 / Details: 2.3M AMMONIUM SULFATE, 0.1M HEPES-NA PH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.33→56 Å / Num. obs: 11309 / % possible obs: 98 % / Observed criterion σ(I): 2.9 / Redundancy: 6.5 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RLG

1rlg


Resolution: 2.33→55.979 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 539 4.8 %
Rwork0.1804 --
obs0.1814 11309 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39 Å2
Refinement stepCycle: LAST / Resolution: 2.33→55.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 568 5 53 1526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071566
X-RAY DIFFRACTIONf_angle_d1.0612250
X-RAY DIFFRACTIONf_dihedral_angle_d13.604672
X-RAY DIFFRACTIONf_chiral_restr0.063276
X-RAY DIFFRACTIONf_plane_restr0.005186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.56450.29531280.22992544X-RAY DIFFRACTION95
2.5645-2.93560.31331370.22162642X-RAY DIFFRACTION99
2.9356-3.69840.21361360.1832701X-RAY DIFFRACTION99
3.6984-55.99510.15581380.16072883X-RAY DIFFRACTION99
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)
10.3911-0.62550.66451.1243-1.49222.2199-0.15050.10750.05790.00450.0893-0.1353-0.16520.01270.05590.2976-0.0860.0110.3679-0.00580.286238.6744.0578-13.6594
25.39341.3266-0.48193.7694-0.51082.5865-0.20530.2253-0.1176-0.22210.27310.26120.2787-0.4798-0.08630.2939-0.09290.01230.34080.07070.260621.8216-10.5725-5.7519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 1:26)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 1:117)

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