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- PDB-5z7q: Crystal structure of Bacillus cereus flagellin -

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Basic information

Entry
Database: PDB / ID: 5z7q
TitleCrystal structure of Bacillus cereus flagellin
ComponentsFlagellin
KeywordsIMMUNE SYSTEM / Bacteria / Flagellin / Adjuvant
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
f41 fragment of flagellin, N-terminal domain / f41 fragment of flagellin, N-terminal domain / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKim, M. / Hong, M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National research foundation of korea2015R1D1A1A01057574 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of Bacillus cereus flagellin and structure-guided fusion-protein designs
Authors: Il Kim, M. / Lee, C. / Park, J. / Jeon, B.Y. / Hong, M.
History
DepositionJan 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellin


Theoretical massNumber of molelcules
Total (without water)18,7751
Polymers18,7751
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9630 Å2
Unit cell
Length a, b, c (Å)112.724, 112.724, 40.190
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 Flagellin


Mass: 18774.639 Da / Num. of mol.: 1 / Fragment: UNP residues 54-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1658 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81FD4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.93 Å3/Da / Density % sol: 68.67 % / Description: rod shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M glycine, pH 10, 0.2M lithium sulfate, 1.2M sodium dihydrogen phosphate, and 0.8M di-potassium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00002 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 25160 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Χ2: 2.354 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.885.50.24512390.9650.1150.2711.754100
1.88-1.925.50.22512680.9680.1060.2491.835100
1.92-1.955.50.18712350.9780.0880.2071.995100
1.95-1.995.50.17512670.9820.0820.1932.056100
1.99-2.045.60.15312370.980.0720.1692.274100
2.04-2.085.50.13212430.9840.0620.1462.277100
2.08-2.145.50.12112620.9860.0570.1332.384100
2.14-2.195.60.11312410.9870.0530.1252.425100
2.19-2.265.50.10412840.9890.0490.1152.491100
2.26-2.335.60.09512230.990.0450.1052.447100
2.33-2.415.60.0912650.990.0420.0992.598100
2.41-2.515.60.08412800.9890.040.0932.501100
2.51-2.635.60.07812380.9920.0370.0872.527100
2.63-2.765.50.07112660.9930.0330.0792.536100
2.76-2.945.60.06512680.9950.0310.0722.507100
2.94-3.165.50.05912750.9940.0280.0652.592100
3.16-3.485.50.05312520.9960.0250.0592.477100
3.48-3.995.50.0512970.9950.0240.0562.55599.9
3.99-5.025.40.04612760.9950.0230.0512.39199.2
5.02-504.90.04612440.9960.0230.0522.45293.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K8W

3k8w


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.626 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.093 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 1211 4.8 %RANDOM
Rwork0.1863 ---
obs0.1867 23911 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 27.198 Å2 / Biso min: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.38 Å2-0 Å2
2---0.77 Å20 Å2
3---2.5 Å2
Refinement stepCycle: final / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 153 1447
Biso mean---33.77 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021387
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9611903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9385206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26626.39361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83315254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.087158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021037
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 98 -
Rwork0.189 1738 -
all-1836 -
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)
16.18982.61290.8021.20620.4550.2474-0.29360.48680.4465-0.1920.21030.2041-0.10880.05990.08330.0758-0.0476-0.06190.06570.07290.117215.669-41.9854.889
25.56982.4779-0.29881.7916-0.18220.7253-0.0704-0.24710.69260.01510.01240.3224-0.0708-0.12040.0580.04220.0161-0.02550.0694-0.01240.17593.767-45.40613.978
37.46124.35621.31053.0030.88340.3105-0.0251-0.1081-0.0397-0.04890.0113-0.1031-0.01440.00370.01380.0259-0.0033-0.00560.04260.0030.05812.992-52.06711.594
42.0285-2.04934.82282.8289-5.291311.69890.2975-0.1021-0.2170.29990.14520.07420.3735-0.2858-0.44270.5320.0274-0.09930.40720.04040.2208-0.659-73.51613.998
53.9096-2.5793-2.7211.78742.667914.5713-0.2262-0.37230.50730.21780.16-0.27580.0954-0.7870.06630.25750.00210.03410.1628-0.07760.1547-15.559-53.54411.987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A63 - 131
2X-RAY DIFFRACTION2A132 - 179
3X-RAY DIFFRACTION3A180 - 217
4X-RAY DIFFRACTION4A218 - 229
5X-RAY DIFFRACTION5A54 - 62

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