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- PDB-1ory: FLAGELLAR EXPORT CHAPERONE IN COMPLEX WITH ITS COGNATE BINDING PARTNER -

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Basic information

Entry
Database: PDB / ID: 1ory
TitleFLAGELLAR EXPORT CHAPERONE IN COMPLEX WITH ITS COGNATE BINDING PARTNER
Components
  • Flagellin
  • flagellar protein FliS
KeywordsCHAPERONE / flagellar chaperone / cytosolic export chaperone / flagellin / FliS / FliC
Function / homology
Function and homology information


bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / cytosol
Similarity search - Function
Flagellar export chaperone, C-terminal domain / Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Helicase, Ruva Protein; domain 3 / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin ...Flagellar export chaperone, C-terminal domain / Flagellar protein FliS / Flagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / Helicase, Ruva Protein; domain 3 / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / Helix non-globular / Four Helix Bundle (Hemerythrin (Met), subunit A) / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Flagellin / Flagellar protein FliS
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 17, 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 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: flagellar protein FliS
B: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8984
Polymers21,7082
Non-polymers1902
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-36 kcal/mol
Surface area8630 Å2
MethodPISA
2
A: flagellar protein FliS
B: Flagellin
hetero molecules

A: flagellar protein FliS
B: Flagellin
hetero molecules

A: flagellar protein FliS
B: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,69412
Polymers65,1246
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16250 Å2
ΔGint-153 kcal/mol
Surface area21780 Å2
MethodPISA
3
A: flagellar protein FliS
B: Flagellin
hetero molecules

A: flagellar protein FliS
B: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7968
Polymers43,4164
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation42_654-x+7/4,z+1/4,y-1/41
Buried area9570 Å2
ΔGint-82 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.241, 166.241, 166.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
DetailsThe biological assembly is a heterodimer

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Components

#1: Protein flagellar protein FliS


Mass: 15534.850 Da / Num. of mol.: 1 / Mutation: M12Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: FliS / Plasmid: pKM1384 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), pRIL / References: UniProt: O67806
#2: Protein Flagellin


Mass: 6173.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: FLAA OR FLIC OR AQ_1998 / Plasmid: pKM1384 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), pRIL / References: UniProt: O67803
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 4.81 Å3/Da / Density % sol: 74.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% isopropanol, 200mM Lithium sulfate, citrate-phosphate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.5
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-BM
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002 / Details: mirrors
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.45→27.7 Å / Num. all: 14386 / Num. obs: 14386 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.046 / Net I/σ(I): 15.66
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.99 / Num. unique all: 1610 / Rsym value: 0.45 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Num. obs: 13539 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.0445
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.7 Å / % possible obs: 99.9 % / Redundancy: 4.8 % / Num. unique obs: 1492 / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.79

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OQP

1oqp


Resolution: 2.45→27.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.295 / SU ML: 0.144 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.229 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26341 721 5 %RANDOM
Rwork0.21454 ---
all0.218 14339 --
obs0.21694 14339 97.39 %-
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: 51.773 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.45→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 10 103 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221331
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.9871792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6925157
X-RAY DIFFRACTIONr_chiral_restr0.1720.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02949
X-RAY DIFFRACTIONr_nbd_refined0.2550.2654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.215
X-RAY DIFFRACTIONr_mcbond_it2.6661.5791
X-RAY DIFFRACTIONr_mcangle_it4.56321286
X-RAY DIFFRACTIONr_scbond_it7.5323540
X-RAY DIFFRACTIONr_scangle_it11.5884.5506
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 59
Rwork0.301 1000
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 100 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.06
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1

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