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- PDB-4kdd: Structure of Mycobacterium tuberculosis ribosome recycling factor... -

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Basic information

Entry
Database: PDB / ID: 4kdd
TitleStructure of Mycobacterium tuberculosis ribosome recycling factor in presence of detergent
ComponentsRibosome-recycling factor
KeywordsTRANSLATION / eubacteria / Ribosome recycling / 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: 1.9 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 24, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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)21,5694
Polymers20,8621
Non-polymers7073
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.370, 33.720, 61.510
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 20861.664 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 52.37 %
Crystal growTemperature: 298 K / Method: under oil in microbatch plates / pH: 7.8
Details: 6% polyethylene glycol 4000, 100mM Tris HCl, 0.6mM Cadmium acetate, 5% polyethylene glycol 400, pH 7.8, Under oil in microbatch plates, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.514 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.9→33.74 Å / Num. all: 17141 / Num. obs: 17141 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.133
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 7.2 / Num. unique all: 17141 / % possible all: 99.9

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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: 1.9→33.7 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.44 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27048 878 5.1 %RANDOM
Rwork0.2494 ---
obs0.25052 16250 99.91 %-
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: 26.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.66 Å2
2--0.45 Å20 Å2
3----0.18 Å2
Refine analyzeLuzzati coordinate error free: 0.167 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 15 195 1644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191463
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9791968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4495183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16723.80371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49815271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0221517
X-RAY DIFFRACTIONr_chiral_restr0.0710.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211091
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 62 -
Rwork0.483 1199 -
obs--100 %
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)
15.61642.56285.80161.29842.55226.16150.13450.1063-0.10380.06560.0469-0.00790.23130.1556-0.18140.12790.0288-0.00170.1221-0.00370.064127.919911.04633.7206
22.3329-1.897-2.59793.32150.89563.8105-0.19580.0295-0.10050.17740.015-0.0440.220.05890.18070.04860.00680.00910.1554-0.03410.019553.22379.237547.6654
32.35570.18623.25210.26840.57364.8866-0.0829-0.00720.1147-0.0582-0.0247-0.0276-0.1692-0.02760.10760.1226-0.0440.02190.11540.00620.046627.053920.894435.1394
45.29940.55495.20920.10320.73195.97490.0679-0.17390.00390.0122-0.04480.00230.1209-0.1899-0.02310.1214-0.0110.01260.0815-0.00350.065519.78515.110338.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 29
2X-RAY DIFFRACTION2A30 - 102
3X-RAY DIFFRACTION3A103 - 148
4X-RAY DIFFRACTION4A149 - 184

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