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- PDB-3b1s: Crystal structure of the cytoplasmic domain of FlhB from Aquifex ... -

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Basic information

Entry
Database: PDB / ID: 3b1s
TitleCrystal structure of the cytoplasmic domain of FlhB from Aquifex aeolicus
Components(Flagellar biosynthetic protein flhB) x 2
KeywordsPROTEIN TRANSPORT / flagella / type III secretion system / membrane protein
Function / homology
Function and homology information


bacterial-type flagellum assembly / protein secretion / plasma membrane
Similarity search - Function
Flagellar biosynthetic protein FlhB / secretion proteins EscU / name from scop / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthetic protein FlhB
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsMeshcheryakov, V.A. / Samatey, F.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins
Authors: Meshcheryakov, V.A. / Kitao, A. / Matsunami, H. / Samatey, F.A.
History
DepositionJul 8, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Mar 13, 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

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Assembly

Deposited unit
A: Flagellar biosynthetic protein flhB
C: Flagellar biosynthetic protein flhB
E: Flagellar biosynthetic protein flhB
B: Flagellar biosynthetic protein flhB
D: Flagellar biosynthetic protein flhB
F: Flagellar biosynthetic protein flhB


Theoretical massNumber of molelcules
Total (without water)47,4996
Polymers47,4996
Non-polymers00
Water86548
1
A: Flagellar biosynthetic protein flhB
B: Flagellar biosynthetic protein flhB


Theoretical massNumber of molelcules
Total (without water)15,8332
Polymers15,8332
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-18 kcal/mol
Surface area8200 Å2
MethodPISA
2
C: Flagellar biosynthetic protein flhB
D: Flagellar biosynthetic protein flhB


Theoretical massNumber of molelcules
Total (without water)15,8332
Polymers15,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-20 kcal/mol
Surface area8160 Å2
MethodPISA
3
E: Flagellar biosynthetic protein flhB
F: Flagellar biosynthetic protein flhB


Theoretical massNumber of molelcules
Total (without water)15,8332
Polymers15,8332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-20 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.600, 33.750, 122.370
Angle α, β, γ (deg.)90.00, 107.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Flagellar biosynthetic protein flhB


Mass: 6174.462 Da / Num. of mol.: 3 / Fragment: C-terminal domain, residues 213-263
Source method: isolated from a genetically manipulated source
Details: auto-cleaved between residues 263 and 264 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: flhB / Production host: Escherichia coli (E. coli) / References: UniProt: O67813
#2: Protein Flagellar biosynthetic protein flhB


Mass: 9658.538 Da / Num. of mol.: 3 / Fragment: C-terminal domain, residues 264-350
Source method: isolated from a genetically manipulated source
Details: auto-cleaved between residues 263 and 264 / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: flhB / Production host: Escherichia coli (E. coli) / References: UniProt: O67813
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3748.15
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2M sodium thiocyanate, 20% PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.9791, 0.97936, 0.99508, 0.96413
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDFeb 16, 2011
RAYONIX MX225HE2CCDFeb 16, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97911
30.979361
40.995081
50.964131
ReflectionResolution: 2.55→47.76 Å / Num. all: 14910 / Num. obs: 14910
Reflection shellResolution: 2.55→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.55→29.75 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.552 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26195 757 5.1 %RANDOM
Rwork0.24122 ---
obs0.24228 14135 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.11 Å2
2--0.78 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 0 48 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0232752
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9973700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.423.10387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.73515553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7141518
X-RAY DIFFRACTIONr_chiral_restr0.1160.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211906
X-RAY DIFFRACTIONr_mcbond_it1.0491.51745
X-RAY DIFFRACTIONr_mcangle_it1.95722844
X-RAY DIFFRACTIONr_scbond_it2.48131007
X-RAY DIFFRACTIONr_scangle_it4.5024.5856
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 50 -
Rwork0.361 1040 -
obs--100 %

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