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- PDB-3gty: Promiscuous Substrate Recognition in Folding and Assembly Activit... -

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Basic information

Entry
Database: PDB / ID: 3gty
TitlePromiscuous Substrate Recognition in Folding and Assembly Activities of the Trigger Factor Chaperone
Components
  • 30S ribosomal protein S7
  • Trigger factor
KeywordsChaperone/Ribosomal protein / Chaperone-Client Complex / Cell cycle / Cell division / Chaperone / Isomerase / Rotamase / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Chaperone-Ribosomal protein COMPLEX
Function / homology
Function and homology information


'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / ribosomal small subunit assembly ...'de novo' cotranslational protein folding / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / regulation of DNA-templated transcription elongation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / cell cycle / translation / cell division / mRNA binding / DNA binding / cytoplasm
Similarity search - Function
Trigger factor, domain 2 / Trigger factor, C-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal domain / Trigger factor ribosome-binding domain / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) ...Trigger factor, domain 2 / Trigger factor, C-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal domain / Trigger factor ribosome-binding domain / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Chitinase A; domain 3 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
30S ribosomal protein S7 / Trigger factor
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsMartinez-Hackert, E. / Hendrickson, W.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone
Authors: Martinez-Hackert, E. / Hendrickson, W.A.
History
DepositionMar 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Trigger factor
S: 30S ribosomal protein S7


Theoretical massNumber of molelcules
Total (without water)68,1732
Polymers68,1732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Trigger factor


Theoretical massNumber of molelcules
Total (without water)51,0491
Polymers51,0491
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
S: 30S ribosomal protein S7


Theoretical massNumber of molelcules
Total (without water)17,1241
Polymers17,1241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.162, 94.162, 193.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Trigger factor / TF


Mass: 51048.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tig, TM_0694 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZF8
#2: Protein 30S ribosomal protein S7


Mass: 17124.018 Da / Num. of mol.: 1 / Fragment: sequence database residues 9-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rpsG, TM_1504 / Plasmid: pet24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38526

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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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 5-10 % PEG4000, 100 NaOAc, pH 5.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792,0.9794,0.9687
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2005 / Details: monochromator
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.96871
ReflectionRedundancy: 3.4 % / Av σ(I) over netI: 21.37 / Number: 82959 / Rmerge(I) obs: 0.058 / Χ2: 1.11 / D res high: 3.3 Å / D res low: 50 Å / Num. obs: 24689 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.15094.710.0221.0643.3
5.647.199.710.0350.8763.4
4.935.6499.910.0410.8933.4
4.484.9310010.0420.9313.4
4.164.4810010.0531.0523.4
3.914.1610010.0890.9563.4
3.723.9110010.1881.3423.4
3.553.7299.510.2882.4273
3.423.5599.910.30.8763.4
3.33.4299.910.4020.8413.4
ReflectionResolution: 3.3→50 Å / Num. obs: 13240 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Χ2: 1.059 / Net I/σ(I): 21.369
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.423.40.36924670.808199.9
3.42-3.553.40.28924810.886199.9
3.55-3.7230.26324762.15199.5
3.72-3.913.40.17824971.2981100
3.91-4.163.40.08424560.9461100
4.16-4.483.40.05124981.004199.9
4.48-4.933.40.04124670.917199.6
4.93-5.643.40.03924400.839198.9
5.64-7.13.40.03424180.89197
7.1-503.20.02222241.016188.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97925.05-8.48
13 wavelength20.97943.53-7.96
13 wavelength30.96873.4-2.21
Phasing dmFOM : 0.67 / FOM acentric: 0.66 / FOM centric: 0.69 / Reflection: 13240 / Reflection acentric: 10986 / Reflection centric: 2254
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.4-39.0790.970.980.95612382230
5.9-9.40.910.920.8718741411463
4.7-5.90.840.850.7722731851422
4.1-4.70.770.780.7322491895354
3.5-4.10.550.550.5338933381512
3.3-3.50.310.310.3223392066273

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 3.4→12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.799 / WRfactor Rfree: 0.34 / WRfactor Rwork: 0.294 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.732 / SU B: 99.135 / SU ML: 0.708 / SU R Cruickshank DPI: 0.666 / SU Rfree: 0.751 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.725 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.329 620 5.2 %RANDOM
Rwork0.257 ---
obs0.261 11963 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.72 Å2 / Biso mean: 49.985 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4610 0 0 0 4610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224673
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9976276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9095558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.82124.468235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.11615966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0171546
X-RAY DIFFRACTIONr_chiral_restr0.0830.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023457
X-RAY DIFFRACTIONr_nbd_refined0.260.22182
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.25
X-RAY DIFFRACTIONr_mcbond_it0.8331.52912
X-RAY DIFFRACTIONr_mcangle_it1.40924550
X-RAY DIFFRACTIONr_scbond_it1.3531997
X-RAY DIFFRACTIONr_scangle_it2.3234.51726
LS refinement shellResolution: 3.4→3.481 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 37 -
Rwork0.335 774 -
all-811 -
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)
14.48744.60983.95717.8984.4537.06070.9080.7949-0.71520.75730.0407-0.3950.58810.8503-0.94860.7225-0.0961-0.26460.6132-0.24520.3596-5.0225.05519.433
21.63290.84682.27330.88681.04374.6635-0.1679-0.0775-0.1597-0.12330.1142-0.06390.1373-0.02040.05370.7362-0.23730.10230.6465-0.02120.393515.22625.3653.133
311.71224.94463.00474.0482.20044.3604-0.1599-0.27190.18010.27470.11930.0594-0.3859-0.1250.04060.74660.1817-0.030.55570.01550.31197.31723.28597.145
46.12232.9433-1.825111.424-0.88092.1565-0.65880.5602-0.5397-0.12260.42560.152-0.00610.03280.23320.532-0.34090.21440.7812-0.10490.22471.77623.77962.978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 112
2X-RAY DIFFRACTION2X113 - 146
3X-RAY DIFFRACTION2X231 - 414
4X-RAY DIFFRACTION3X147 - 230
5X-RAY DIFFRACTION4S8 - 154

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