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- PDB-5dmb: Crystal structure of a translational regulator bound to a flagell... -

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Basic information

Entry
Database: PDB / ID: 5dmb
TitleCrystal structure of a translational regulator bound to a flagellar assembly factor
Components
  • Carbon storage regulator homolog
  • Flagellar assembly factor FliW
KeywordsTRANSLATION / flagellum / assembly factor
Function / homology
Function and homology information


regulation of bacterial-type flagellum assembly / regulation of carbohydrate metabolic process / bacterial-type flagellum organization / mRNA catabolic process / bacterial-type flagellum assembly / negative regulation of translational initiation / mRNA 5'-UTR binding / regulation of translation / cytosol / cytoplasm
Similarity search - Function
BH3618-like / BH3618-like / Flagellar assembly factor FliW / Flagellar assembly factor FliW domain superfamily / FliW protein / Translational regulator CsrA / Carbon storage regulator superfamily / Global regulator protein family / Roll / Mainly Beta
Similarity search - Domain/homology
Translational regulator CsrA / Flagellar assembly factor FliW
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsAltegoer, F. / Bange, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein.
Authors: Altegoer, F. / Rensing, S.A. / Bange, G.
History
DepositionSep 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar assembly factor FliW
D: Carbon storage regulator homolog


Theoretical massNumber of molelcules
Total (without water)26,5392
Polymers26,5392
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-14 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.876, 61.681, 42.902
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Flagellar assembly factor FliW


Mass: 17389.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Gene: fliW, GTNG_3059 / Plasmid: pET24d(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4ISV0
#2: Protein Carbon storage regulator homolog


Mass: 9149.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Gene: csrA, GTNG_3058 / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4ISU9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium fluoride, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.3→42.48 Å / Num. obs: 11552 / % possible obs: 99.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 1.8
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.518

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJ7

2aj7


Resolution: 2.301→42.477 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 602 5.21 %
Rwork0.224 --
obs0.2275 11552 91.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→42.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 0 73 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091723
X-RAY DIFFRACTIONf_angle_d1.3962338
X-RAY DIFFRACTIONf_dihedral_angle_d17.894645
X-RAY DIFFRACTIONf_chiral_restr0.049280
X-RAY DIFFRACTIONf_plane_restr0.006300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3005-2.5320.40861170.30852384X-RAY DIFFRACTION80
2.532-2.89830.34091480.28332685X-RAY DIFFRACTION91
2.8983-3.65130.31531580.24032901X-RAY DIFFRACTION97
3.6513-42.48370.24691790.1892980X-RAY DIFFRACTION99

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