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- PDB-5xef: Crystal structure of flagellar chaperone from bacteria -

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Basic information

Entry
Database: PDB / ID: 5xef
TitleCrystal structure of flagellar chaperone from bacteria
ComponentsFlagellar protein fliS
KeywordsCHAPERONE / flagellar chaperone / bacteria
Function / homologyFlagellar protein FliS / Flagellar protein FliS superfamily / Flagellar protein FliS / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / cytosol / Flagellar protein fliS
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLee, C. / Hong, M.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
the Ministry of Science, ICT & Future Planning2015R1D1A1A01057574 Korea, Republic Of
the Ministry of Health & WelfareHI15C2890 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of the flagellar chaperone FliS from Bacillus cereus and an invariant proline critical for FliS dimerization and flagellin recognition
Authors: Lee, C. / Kim, M.I. / Park, J. / Jeon, B.Y. / Yoon, S.I. / Hong, M.
History
DepositionApr 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flagellar protein fliS


Theoretical massNumber of molelcules
Total (without water)14,8941
Polymers14,8941
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8390 Å2
Unit cell
Length a, b, c (Å)83.207, 83.207, 47.771
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Flagellar protein fliS


Mass: 14894.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1639 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81FF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.5 M ammonium sulfate 4 % isopropanol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97973 Å
DetectorType: ADSC QUANTUM 1 / Detector: AREA DETECTOR / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97973 Å / Relative weight: 1
ReflectionResolution: 2→72.06 Å / Num. obs: 18292 / % possible obs: 100 % / Redundancy: 18.4 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.023 / Rrim(I) all: 0.095 / Χ2: 2.769 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.05180.1860.9950.0460.1922.115100
2.05-2.1118.70.1740.9930.0420.1792.413100
2.11-2.1719.60.1540.9960.0360.1592.783100
2.17-2.2419.40.1410.9970.0330.1452.943100
2.24-2.32190.1320.9960.0310.1353.06399.9
2.32-2.4218.40.1220.9980.030.1253.136100
2.42-2.53170.1180.9970.030.1223.382100
2.53-2.6618.80.1120.9970.0270.1153.578100
2.66-2.8318.80.1030.9970.0250.1063.807100
2.83-3.04180.0940.9980.0230.0974.121100
3.04-3.3516.20.0850.9970.0220.0884.21899.8
3.35-3.8317.80.0760.9990.0180.0784.21799.9
3.83-4.8316.40.070.9980.0170.0724.258100
4.83-5015.70.0680.9990.0170.0714.20599.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→72.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.116 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.141
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 642 5 %RANDOM
Rwork0.1939 ---
obs0.1955 12238 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.37 Å2 / Biso mean: 26.035 Å2 / Biso min: 13.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å2-0.7 Å2-0 Å2
2---1.4 Å20 Å2
3---4.53 Å2
Refinement stepCycle: final / Resolution: 2→72.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 0 100 1132
Biso mean---33 -
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021048
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9881413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0945122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46525.78957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12215196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.402156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02777
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 47 -
Rwork0.217 900 -
all-947 -
obs--100 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

ID
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2
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4
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