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- PDB-4kb2: Crystal structure of ribosome recycling factor mutant R109A from ... -

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Basic information

Entry
Database: PDB / ID: 4kb2
TitleCrystal structure of ribosome recycling factor mutant R109A from Mycobacterium tuberculosis
ComponentsRibosome-recycling factor
KeywordsTRANSLATION / Ribosome recycling factor / ribosomes / eubacteria / post-termination complex / Elongation factor G / Bacterial cytosol
Function / homology
Function and homology information


translation termination factor activity / ribosomal large subunit binding / translational termination / peptidoglycan-based cell wall / translation / plasma membrane / cytoplasm
Similarity search - Function
Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle ...Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Ribosome-recycling factor / Ribosome-recycling factor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSelvaraj, M. / Govindan, A. / Seshadri, A. / Dubey, B. / Varshney, U. / Vijayan, M.
CitationJournal: J.Biosci. / Year: 2013
Title: Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants.
Authors: Selvaraj, M. / Govindan, A. / Seshadri, A. / Dubey, B. / Varshney, U. / Vijayan, M.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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_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_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_ref_seq_dif.details / _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: Ribosome-recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1134
Polymers20,7761
Non-polymers3373
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.490, 33.740, 61.150
Angle α, β, γ (deg.)90.00, 113.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosome-recycling factor


Mass: 20775.549 Da / Num. of mol.: 1 / Mutation: R109A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: frr, MT2949, MTCY274.13c, Rv2882c / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P66734, UniProt: P9WGY1*PLUS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 298 K / Method: under oil using microbatch plates / pH: 7.8
Details: 6% Polyethylene glycol 4000, 20mM Tris-HCl (pH 7.8), 0.6mM Cadmium acetate, 5% Polyethylene glycol 400, Under oil using microbatch plates, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 23, 2011 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.3→56.2 Å / Num. obs: 9680 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 6.9 / Num. unique all: 9680

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WQG

1wqg


Resolution: 2.3→51.97 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.874 / SU B: 11.792 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26686 448 4.6 %RANDOM
Rwork0.22613 ---
obs0.2279 9227 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.023 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å2-0.8 Å2
2--0.09 Å2-0 Å2
3----1.01 Å2
Refine analyzeLuzzati coordinate error free: 0.376 Å
Refinement stepCycle: LAST / Resolution: 2.3→51.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 3 102 1543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191453
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9741959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2375183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.34824.44472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7815275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8451515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211089
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 31 -
Rwork0.315 695 -
obs--99.86 %
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)
14.38111.21622.92831.41240.83392.1718-0.0885-0.0429-0.1774-0.02650.1947-0.04380.0290.0598-0.10620.06540.02390.02090.0798-0.00610.056627.738110.930733.0751
21.4361-0.03581.92790.09480.07662.9592-0.1354-0.00070.0985-0.07310.0116-0.0089-0.21560.05090.12380.0987-0.0090.01210.0680.00450.076726.604520.937334.6514
34.9460.23335.39730.04170.35816.8718-0.0399-0.20310.02890.0049-0.02610.0422-0.0843-0.15280.06610.058-0.01910.00930.0647-0.00510.098719.384215.149537.8532
43.6068-1.2279-6.21014.53151.851110.9232-0.34630.0027-0.12140.48010.046-0.12390.4330.04650.30030.124-0.0097-0.05990.0892-0.00820.067252.91649.114847.4053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A103 - 148
3X-RAY DIFFRACTION3A149 - 184
4X-RAY DIFFRACTION4A30 - 102

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