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- PDB-1orj: FLAGELLAR EXPORT CHAPERONE -

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Basic information

Entry
Database: PDB / ID: 1orj
TitleFLAGELLAR EXPORT CHAPERONE
Componentsflagellar protein FliSFlagellum
KeywordsCHAPERONE / flagellin / flagellar export / flagellum / four helix bundle
Function / homology
Function and homology information


bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / cytosol
Similarity search - Function
Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar protein FliS
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.25 Å
AuthorsEvdokimov, A.G. / Phan, J. / Tropea, J.E. / Routzahn, K.M. / Peters III, H.K. / Pokross, M. / Waugh, D.S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Similar modes of polypeptide recognition by export chaperones in flagellar biosynthesis and type III secretion
Authors: Evdokimov, A.G. / Phan, J. / Tropea, J.E. / Routzahn, K.M. / Peters III, H.K. / Pokross, M. / Waugh, D.S.
History
DepositionMar 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: flagellar protein FliS
B: flagellar protein FliS
C: flagellar protein FliS
D: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)62,1524
Polymers62,1524
Non-polymers00
Water5,098283
1
A: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)15,5381
Polymers15,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)15,5381
Polymers15,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)15,5381
Polymers15,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)15,5381
Polymers15,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: flagellar protein FliS
B: flagellar protein FliS
C: flagellar protein FliS
D: flagellar protein FliS

A: flagellar protein FliS
B: flagellar protein FliS
C: flagellar protein FliS
D: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)124,3038
Polymers124,3038
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17720 Å2
ΔGint-71 kcal/mol
Surface area39260 Å2
MethodPISA
6
A: flagellar protein FliS
D: flagellar protein FliS

B: flagellar protein FliS
C: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)62,1524
Polymers62,1524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5490 Å2
ΔGint-27 kcal/mol
Surface area23000 Å2
MethodPISA
7
A: flagellar protein FliS
D: flagellar protein FliS


Theoretical massNumber of molelcules
Total (without water)31,0762
Polymers31,0762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-13 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.070, 131.760, 74.898
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-5255-

HOH

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Components

#1: Protein
flagellar protein FliS / Flagellum


Mass: 15537.916 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: FliS / Plasmid: pKM1234, pDEST-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), pRIL / References: UniProt: O67806
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.72 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2.0M Ammonium sulfate, 100mM MES, 2mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMMES1droppH6.5
3150 mM1dropNaCl
42 mMdithiothreitol1drop
52.0 Mammonium sulfate1reservoir
6100 mMMES1reservoirpH5.4-6.2., or cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 20, 2002 / Details: mirrors
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→43 Å / Num. all: 39636 / Num. obs: 39636 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.0568 / Rsym value: 0.0456 / Net I/σ(I): 14.31
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 4.04 / Num. unique all: 4865 / Rsym value: 0.253 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 100 Å / Num. obs: 44213 / % possible obs: 94.9 % / Redundancy: 3.25 % / Rmerge(I) obs: 0.0473
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 94.3 % / Redundancy: 2.29 % / Num. unique obs: 5127 / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.65

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
SHELXLrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.25→43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.028 / SU ML: 0.125 / Isotropic thermal model: isotropic per atom / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24703 2011 5.1 %RANDOM
Rwork0.18867 ---
all0.19163 39635 --
obs0.19163 37624 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.682 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---1.65 Å20 Å2
3----0.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.191 Å0.194 Å
Refinement stepCycle: LAST / Resolution: 2.25→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 0 283 4130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223892
X-RAY DIFFRACTIONr_angle_refined_deg2.4461.9815232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6315456
X-RAY DIFFRACTIONr_chiral_restr0.2180.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022766
X-RAY DIFFRACTIONr_nbd_refined0.2610.21845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4790.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3280.225
X-RAY DIFFRACTIONr_mcbond_it5.2391.52296
X-RAY DIFFRACTIONr_mcangle_it7.3123746
X-RAY DIFFRACTIONr_scbond_it10.72331596
X-RAY DIFFRACTIONr_scangle_it15.6754.51486
LS refinement shellResolution: 2.25→2.31 Å / Rfactor Rfree error: 133 / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 -
Rwork0.22 2804
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 100 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.05
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.7

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