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- PDB-4qxl: Crystal Structure of FLHE -

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Basic information

Entry
Database: PDB / ID: 4qxl
TitleCrystal Structure of FLHE
ComponentsFlagellar protein flhE
KeywordsMOTOR PROTEIN / beta-sandwich / flagellar type III secretion system / periplasmic / secretion pore plug
Function / homology:
Function and homology information
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.512 Å
AuthorsLee, J. / Monzingo, A.F. / Keatinge-Clay, A.T. / Harshey, R.M.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure of Salmonella FlhE, Conserved Member of a Flagellar Type III Secretion Operon.
Authors: Lee, J. / Monzingo, A.F. / Keatinge-Clay, A.T. / Harshey, R.M.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 protein flhE


Theoretical massNumber of molelcules
Total (without water)13,0331
Polymers13,0331
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.425, 36.755, 111.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flagellar protein flhE


Mass: 13032.729 Da / Num. of mol.: 1 / Fragment: UNP residues 17-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: FLHE, SEEA0014_18915 / Plasmid: pTrc99a / Production host: Salmonella enterica (bacteria) / Strain (production host): ST004 / References: UniProt: X5B9E9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M sodium chloride, 10% ethanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00506 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00506 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 15949 / % possible obs: 92.3 % / Redundancy: 9.6 % / Biso Wilson estimate: 11.89 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.687 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.51-1.547.70.2636880.69180.2
1.54-1.569.10.2138030.743198.4
1.56-1.599.50.1948500.783197.5
1.59-1.6310.30.187820.827197.1
1.63-1.669.70.1568541.021197.9
1.66-1.79.90.148280.98198.1
1.7-1.749.70.1278281.177199
1.74-1.799.80.1158471.414198.9
1.79-1.849.90.1118381.494197.3
1.84-1.99.40.1047342.001187.7
1.9-1.976.60.1046132.351171
1.97-2.059.80.0778472.125199.9
2.05-2.149.80.078572.325199.8
2.14-2.269.40.076052.456170.8
2.26-2.49.50.0667022.385181.3
2.4-2.5810.10.0638722.204199.8
2.58-2.8410.40.0618972.4741100
2.84-3.2510.60.0558702.5321100
3.25-4.18.70.0416732.067173.6
4.1-50100.049611.748197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.512→34.906 Å / FOM work R set: 0.8555 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 800 5.05 %RANDOM
Rwork0.1999 ---
obs0.2012 15847 92.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.21 Å2 / Biso mean: 14.25 Å2 / Biso min: 4.8 Å2
Refinement stepCycle: LAST / Resolution: 1.512→34.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 0 86 941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007876
X-RAY DIFFRACTIONf_angle_d1.2171192
X-RAY DIFFRACTIONf_chiral_restr0.081132
X-RAY DIFFRACTIONf_plane_restr0.005156
X-RAY DIFFRACTIONf_dihedral_angle_d11.345314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.512-1.60660.23921450.18452542268796
1.6066-1.73060.21711340.18332601273598
1.7306-1.90480.21561350.19622464259997
1.9048-2.18030.22511350.20232479261492
2.1803-2.74680.22931240.22232320244485
2.7468-34.91560.22591270.19542641276891

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