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- PDB-1oms: Structure determination by MAD: E.coli Trigger Factor binding at ... -

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Basic information

Entry
Database: PDB / ID: 1oms
TitleStructure determination by MAD: E.coli Trigger Factor binding at the ribosomal exit tunnel.
ComponentsTrigger Factor
KeywordsISOMERASE / alpha-beta structure
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein transport ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein transport / ribosome binding / response to heat / cell division / identical protein binding / membrane / cytosol
Similarity search - Function
Trigger factor ribosome-binding domain / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. ...Trigger factor ribosome-binding domain / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SULFUR DIOXIDE / Trigger factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKristensen, O. / Gajhede, M.
Citation
Journal: Structure / Year: 2003
Title: Chaperone binding at the ribosomal exit tunnel.
Authors: Kristensen, O. / Gajhede, M.
#1: Journal: Nature / Year: 2002
Title: L23 protein functions as a chaperone docking site on the ribosome.
Authors: Kramer, G. / Rauch, T. / Rist, W. / Vorderwulbecke, S. / Patzelt, H. / Schulze-Specking, A. / Ban, N. / Deuerling, E. / Bukau, B.
#2: Journal: J.Mol.Biol. / Year: 2003
Title: Localization of the Trigger Factor Binding Site on the Ribosomal 50S Subunit.
Authors: Blaha, G. / Wilson, D.N. / Stoller, G. / Fischer, G. / Willumeit, R. / Nierhaus, K.H.
#3: Journal: J.Mol.Biol. / Year: 2003
Title: Interaction of trigger factor with the ribosome.
Authors: Maier, R. / Eckert, B. / Scholz, C. / Lilie, H. / Schmid, F.X.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Nov 13, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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: Trigger Factor
B: Trigger Factor
C: Trigger Factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,89123
Polymers40,5153
Non-polymers2,37620
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-153 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.644, 71.644, 375.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-601-

SO2

21B-601-

SO2

31B-622-

HOH

41B-639-

HOH

51C-543-

HOH

61C-594-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Trigger Factor


Mass: 13504.907 Da / Num. of mol.: 3 / Fragment: Ribosome binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tig / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A850, peptidylprolyl isomerase

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Non-polymers , 5 types, 234 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 2000 MME, PEG 400, ammonium sulfate, sodium acetate, tris, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mg/mlprotein1drop
230 %PEG2000 MME1reservoir
385 mMsodium acetate1reservoir
4100 mMTris-base1reservoir
515 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9797, 0.9404
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2002
RadiationMonochromator: sagittal-focusing double crystal monochromator in combination with a vertical focusing mirror.
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.94041
ReflectionResolution: 2.3→30 Å / Num. obs: 17023 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 33.3
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2432 / Rsym value: 0.33 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 31810 / Redundancy: 4.2 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5499572.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement was based on the "mlhl" target function. Experimental phases and strong NCS restraints were used throughout. Used all data in the ultimate brief refinement cycle against a ...Details: Refinement was based on the "mlhl" target function. Experimental phases and strong NCS restraints were used throughout. Used all data in the ultimate brief refinement cycle against a standard crystallographic target: R-factor(all).
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2044 6.4 %SHELLS
Rwork0.208 ---
obs0.208 31810 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9718 Å2 / ksol: 0.353647 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å23.96 Å20 Å2
2--4.66 Å20 Å2
3----9.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 139 214 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.72.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 305 5.7 %
Rwork0.245 5011 -
obs-5011 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SO2.PARAMSO2.TOP
X-RAY DIFFRACTION5PG4.PARAMPG4.TOP
X-RAY DIFFRACTION6GOL.PARAMGOL.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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