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- PDB-1p9y: Ribosome binding of E. coli Trigger Factor mutant F44L. -

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Basic information

Entry
Database: PDB / ID: 1p9y
TitleRibosome binding of E. coli Trigger Factor mutant F44L.
ComponentsTrigger factor
KeywordsISOMERASE / ALPHA-BETA PROTEIN
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 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 ...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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Trigger factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionMay 13, 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: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8415
Polymers26,6602
Non-polymers1803
Water3,765209
1
A: Trigger factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3902
Polymers13,3301
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trigger factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4503
Polymers13,3301
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.901, 71.901, 257.659
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
11A-1101-

HOH

21A-1106-

HOH

31A-1110-

HOH

41B-1052-

HOH

51B-1099-

HOH

DetailsEach of the separate chains A and B represent a biological relevant unit.

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Components

#1: Protein Trigger factor / TF


Mass: 13330.205 Da / Num. of mol.: 2 / Fragment: Ribosome binding domain / Mutation: F44L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TIG / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A850, peptidylprolyl isomerase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.25 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 2000 MME, AMMONIUM SULFATE, SODIUM ACETATE, TRIS, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoirpH5.0
45 %PEG4001reservoir
55 %glycerol1reservoir
631 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.12 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 13, 2001
RadiationMonochromator: Bendable asymmetrically cut Si(111) crystal in combination with vertically focusing cylindrical mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 14381 / Num. obs: 14381 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 25.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 6.5 / Num. unique all: 1366 / Rsym value: 0.201 / % possible all: 96.7
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMS

1oms


Resolution: 2.15→35.95 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 348074.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement was vased on the "MLF"target function 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
Rfree0.247 1421 10.1 %SHELLS
Rwork0.2 ---
obs0.2 14073 97.5 %-
all-14381 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2016 Å2 / ksol: 0.382659 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å24.05 Å20 Å2
2--2.51 Å20 Å2
3----5.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.15→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 221 2033
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.882.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 206 9.2 %
Rwork0.191 2038 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACY.PARAMACY.TOP
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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