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- PDB-3b0z: Crystal structure of cytoplasmic domain of FlhB from Salmonella t... -

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Basic information

Entry
Database: PDB / ID: 3b0z
TitleCrystal structure of cytoplasmic domain of FlhB from Salmonella typhimurium
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 / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2080 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2080 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Flagellar biosynthetic protein FlhB
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.45 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
DepositionJun 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar biosynthetic protein flhB
B: Flagellar biosynthetic protein flhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0056
Polymers18,8292
Non-polymers1774
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.102, 49.102, 143.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Flagellar biosynthetic protein flhB


Mass: 6141.140 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 219-269
Source method: isolated from a genetically manipulated source
Details: auto-cleaved between residues 269 and 270
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: flhB / Production host: Escherichia coli (E. coli) / References: UniProt: P40727
#2: Protein Flagellar biosynthetic protein flhB


Mass: 12687.534 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 270-383 / Mutation: G383A
Source method: isolated from a genetically manipulated source
Details: auto-cleaved between residues 269 and 270
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: flhB / Production host: Escherichia coli (E. coli) / References: UniProt: P40727
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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 (%)
12.2946.32
2
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium cacodylate, 0.2M zinc acetate, 25% propylene glycol, pH 5.0, 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 BL44XU20.97894, 0.97919
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDJul 15, 2010
RAYONIX MX225HE2CCDJul 15, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.978941
30.979191
ReflectionResolution: 2.45→40.45 Å / Num. obs: 6875
Reflection shellResolution: 2.45→2.58 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: 2.45→28.07 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.131 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24709 346 5.1 %RANDOM
Rwork0.23077 ---
obs0.23163 6416 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.147 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 4 20 1016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221013
X-RAY DIFFRACTIONr_angle_refined_deg2.091.9531370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2885123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0123.19147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.00315178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6681510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021767
X-RAY DIFFRACTIONr_mcbond_it0.921.5625
X-RAY DIFFRACTIONr_mcangle_it1.74521001
X-RAY DIFFRACTIONr_scbond_it2.8043388
X-RAY DIFFRACTIONr_scangle_it4.8144.5369
LS refinement shellResolution: 2.453→2.516 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 22 -
Rwork0.278 393 -
obs--99.76 %
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)
12.86473.3859-3.046.1244-5.24566.6661-0.1538-0.3054-0.5064-0.2451-0.0648-0.30590.5336-0.35270.21860.1535-0.0945-0.0370.74050.05550.340635.9695-8.709528.1112
24.2332-0.01581.29184.9885-0.81586.5148-0.0638-0.43310.164-0.18750.12860.1137-0.4167-0.5925-0.06480.05580.04440.04460.4347-0.02140.131138.19119.032912.5737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A229 - 269
2X-RAY DIFFRACTION2B270 - 353

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