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- PDB-1w26: Trigger Factor in Complex with the Ribosome forms a Molecular Cra... -

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Basic information

Entry
Database: PDB / ID: 1w26
TitleTrigger Factor in Complex with the Ribosome forms a Molecular Cradle for Nascent Proteins
ComponentsTRIGGER FACTOR
KeywordsCHAPERONE / PROTEIN FOLDING / RIBOSOME ASSOCIATED PROTEIN / NASCENT CHAIN / CELL DIVISION / ISOMERASE
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / chaperone-mediated protein folding / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosome binding / protein transport / response to heat / cell cycle / cell division / membrane / identical protein binding / cytosol
Similarity search - Function
Trigger factor, domain 2 / Trigger factor, C-terminal domain / 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, domain 2 / Trigger factor, C-terminal domain / 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 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Trigger factor / Trigger factor
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsFerbitz, L. / Maier, T. / Patzelt, H. / Bukau, B. / Deuerling, E. / Ban, N.
CitationJournal: Nature / Year: 2004
Title: Trigger Factor in Complex with the Ribosome Forms a Molecular Cradle for Nascent Proteins
Authors: Ferbitz, L. / Maier, T. / Patzelt, H. / Bukau, B. / Deuerling, E. / Ban, N.
History
DepositionJun 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIGGER FACTOR
B: TRIGGER FACTOR


Theoretical massNumber of molelcules
Total (without water)97,5432
Polymers97,5432
Non-polymers00
Water1,58588
1
A: TRIGGER FACTOR


Theoretical massNumber of molelcules
Total (without water)48,7711
Polymers48,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TRIGGER FACTOR


Theoretical massNumber of molelcules
Total (without water)48,7711
Polymers48,7711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.251, 47.415, 114.831
Angle α, β, γ (deg.)90.00, 113.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIGGER FACTOR / TF


Mass: 48771.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P22257, UniProt: P0A850*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN PROTEIN EXPORT. ACTS AS A CHAPERONE BY MAINTAINING THE NEWLY SYNTHESIZED PROTEIN IN AN ...INVOLVED IN PROTEIN EXPORT. ACTS AS A CHAPERONE BY MAINTAINING THE NEWLY SYNTHESIZED PROTEIN IN AN OPEN CONFORMATION.

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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: 2.56 Å3/Da / Density % sol: 57 %
Crystal growDetails: 22-26% POLYETHYLENEGLYCOL 4000 WITH 14% 1,4-BUTANEDIOL IN 0.1M MES PH 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97879
DetectorDate: Jan 25, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26426 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→45.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 216046.72 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELEHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.324 5057 9.9 %RANDOM
Rwork0.241 ---
obs0.241 51062 100 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 45.9048 Å2 / ksol: 0.302437 e/Å3
Displacement parametersBiso mean: 74.31 Å2
Baniso -1Baniso -2Baniso -3
1-6.92 Å20 Å211.76 Å2
2---6.96 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 0 88 6860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0007
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_deg1.31382
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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