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- PDB-3iqc: Crystal structure of FliS from H. pylori -

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Basic information

Entry
Database: PDB / ID: 3iqc
TitleCrystal structure of FliS from H. pylori
ComponentsFlagellar protein
KeywordsCHAPERONE / flagella / Flagellum
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 secretion chaperone FliS
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLam, W.W.L. / Ling, T.K.W. / Woo, E.J. / Au, S.W.N.
CitationJournal: Faseb J. / Year: 2010
Title: Molecular interaction of flagellar export chaperone FliS and cochaperone HP1076 in Helicobacter pylori
Authors: Lam, W.W.L. / Woo, E.J. / Kotaka, M. / Tam, W.K. / Leung, Y.C. / Ling, T.K.W. / Au, S.W.N.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)29,9402
Polymers29,9402
Non-polymers00
Water19811
1
A: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)14,9701
Polymers14,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flagellar protein


Theoretical massNumber of molelcules
Total (without water)14,9701
Polymers14,9701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.469, 92.469, 144.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 22 - 120 / Label seq-ID: 27 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Flagellar protein / FliS


Mass: 14969.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0753 / Plasmid: pGEX-6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O25448
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1M Hepes, 0.2M NaCl, 25% PEG3350, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorDate: Aug 28, 2006
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→42.68 Å / Num. obs: 8726 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 24.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 3 / Num. unique all: 1270 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ORJ

1orj


Resolution: 2.7→30.14 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.949 / SU B: 32.078 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.365
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2838 415 4.8 %RANDOM
Rwork0.2377 ---
obs0.23992 8287 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 11 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221800
X-RAY DIFFRACTIONr_bond_other_d0.0010.021198
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9692432
X-RAY DIFFRACTIONr_angle_other_deg1.10932933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06225.16989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.30415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5651510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
589MEDIUM POSITIONAL0.110.5
769LOOSE POSITIONAL0.195
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 29 -
Rwork0.305 625 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.94461.5480.70324.65831.61462.92550.0831-0.02270.05970.0896-0.0844-0.2825-0.1330.20910.00130.0165-0.008-0.00650.09060.02620.032337.135-39.87349.831
21.25970.77790.09198.971.8814.00230.09050.12320.3997-0.3393-0.1686-0.0184-0.42590.32040.07810.0628-0.00490.02680.12960.07910.159943.457-22.80737.427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 126
2X-RAY DIFFRACTION2B20 - 120

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