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- PDB-5dmd: Crystal structure of the flagellar assembly factor FliW -

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Basic information

Entry
Database: PDB / ID: 5dmd
TitleCrystal structure of the flagellar assembly factor FliW
ComponentsFlagellar assembly factor FliW
KeywordsTRANSLATION / flagellum / assembly factor
Function / homology
Function and homology information


bacterial-type flagellum assembly / regulation of translation / cytoplasm
Similarity search - Function
BH3618-like / BH3618-like / Flagellar assembly factor FliW / Flagellar assembly factor FliW domain superfamily / FliW protein / Roll / Mainly Beta
Similarity search - Domain/homology
Flagellar assembly factor FliW
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 2.0Jan 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / struct_asym / struct_conf / struct_mon_prot_cis / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar assembly factor FliW
B: Flagellar assembly factor FliW


Theoretical massNumber of molelcules
Total (without water)34,7802
Polymers34,7802
Non-polymers00
Water4,648258
1
A: Flagellar assembly factor FliW


Theoretical massNumber of molelcules
Total (without water)17,3901
Polymers17,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar assembly factor FliW


Theoretical massNumber of molelcules
Total (without water)17,3901
Polymers17,3901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.539, 42.516, 71.917
Angle α, β, γ (deg.)90.00, 102.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagellar assembly factor FliW


Mass: 17389.801 Da / Num. of mol.: 2 / Mutation: P40Q
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 40 % (v/v) PEG 400, 5 % (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.45→46.38 Å / Num. obs: 49625 / % possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.5
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.9 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJ7

2aj7


Resolution: 1.45→46.383 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 2467 4.97 %
Rwork0.2047 --
obs0.2062 49625 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→46.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 0 0 2297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072411
X-RAY DIFFRACTIONf_angle_d1.1383293
X-RAY DIFFRACTIONf_dihedral_angle_d14.899890
X-RAY DIFFRACTIONf_chiral_restr0.069392
X-RAY DIFFRACTIONf_plane_restr0.006424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4498-1.47770.34771290.29822364X-RAY DIFFRACTION91
1.4777-1.50790.31731270.27992590X-RAY DIFFRACTION99
1.5079-1.54070.30891510.2552587X-RAY DIFFRACTION100
1.5407-1.57650.26841540.24852637X-RAY DIFFRACTION100
1.5765-1.61590.28551570.23612563X-RAY DIFFRACTION100
1.6159-1.65960.25721290.23432616X-RAY DIFFRACTION100
1.6596-1.70850.26291270.22942663X-RAY DIFFRACTION100
1.7085-1.76360.27791350.22742624X-RAY DIFFRACTION100
1.7636-1.82660.26591530.21722598X-RAY DIFFRACTION100
1.8266-1.89980.22761370.21072611X-RAY DIFFRACTION100
1.8998-1.98620.23531290.2072654X-RAY DIFFRACTION100
1.9862-2.0910.26931320.19762612X-RAY DIFFRACTION100
2.091-2.2220.22891460.20112634X-RAY DIFFRACTION100
2.222-2.39350.21891270.2062662X-RAY DIFFRACTION100
2.3935-2.63440.24511360.2122652X-RAY DIFFRACTION100
2.6344-3.01550.23871420.20252655X-RAY DIFFRACTION100
3.0155-3.7990.21261280.18982678X-RAY DIFFRACTION100
3.799-46.40640.20951280.18292758X-RAY DIFFRACTION100

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