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- PDB-3mix: Crystal structure of the cytosolic domain of B. subtilis FlhA -

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Basic information

Entry
Database: PDB / ID: 3mix
TitleCrystal structure of the cytosolic domain of B. subtilis FlhA
ComponentsFlagellar biosynthesis protein flhA
KeywordsPROTEIN TRANSPORT / Flagella biosynthesis / type III secretion
Function / homology
Function and homology information


bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin ...Flagellar biosynthesis protein FlhA / FHIPEP family, domain 1 / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthesis protein FlhA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBange, G. / Kuemmerer, N. / Bozkurt, G. / Wild, K. / Sinning, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: FlhA provides the adaptor for coordinated delivery of late flagella building blocks to the type III secretion system.
Authors: Bange, G. / Kummerer, N. / Engel, C. / Bozkurt, G. / Wild, K. / Sinning, I.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar biosynthesis protein flhA


Theoretical massNumber of molelcules
Total (without water)42,7991
Polymers42,7991
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.177, 84.177, 118.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Flagellar biosynthesis protein flhA


Mass: 42798.664 Da / Num. of mol.: 1 / Fragment: CYTOSOLIC DOMAIN (UNP residues 303-677)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU16390, flhA / Plasmid: pet24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P35620
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, pH 6.5, 25 % w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.933
SYNCHROTRONESRF ID14-220.933
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 21, 2009
ADSC QUANTUM 42CCDMar 15, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
21
ReflectionResolution: 2.3→45 Å / Num. all: 20948 / Num. obs: 20948 / % possible obs: 99.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.075 / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3043 / Rsym value: 0.215 / % possible all: 99.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→34.83 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.865 / SU B: 12.524 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26925 1056 5 %RANDOM
Rwork0.21649 ---
obs0.21906 19891 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.816 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 120 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222500
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2882.0013391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02925.586111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47515471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1451514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.51563
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23522547
X-RAY DIFFRACTIONr_scbond_it1.93937
X-RAY DIFFRACTIONr_scangle_it3.2854.5844
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 75 -
Rwork0.234 1350 -
obs--92.41 %
Refinement TLS params.Method: refined / Origin x: 11.786 Å / Origin y: 27.19 Å / Origin z: 7.305 Å
111213212223313233
T0.0975 Å20.0007 Å2-0.0584 Å2-0.0778 Å20.0515 Å2--0.1437 Å2
L2.1734 °2-0.1528 °21.0131 °2-1.9758 °20.447 °2--2.6015 °2
S-0.0832 Å °0.171 Å °0.3329 Å °-0.1245 Å °-0.1249 Å °-0.2794 Å °-0.2863 Å °0.2842 Å °0.208 Å °

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