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- PDB-2zvy: Structure of the periplasmic domain of MotB from Salmonella (crys... -

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Basic information

Entry
Database: PDB / ID: 2zvy
TitleStructure of the periplasmic domain of MotB from Salmonella (crystal form II)
ComponentsChemotaxis protein motB
KeywordsMEMBRANE PROTEIN / 2-layer sandwich / Bacterial flagellum / Cell inner membrane / Cell membrane / Chemotaxis / Flagellar rotation / Membrane / Transmembrane
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent cell motility / chemotaxis
Similarity search - Function
Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / OmpA-like domain / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKojima, S. / Homma, M. / Namba, K. / Imada, K.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB
Authors: Kojima, S. / Imada, K. / Sakuma, M. / Sudo, Y. / Kojima, C. / Minamino, T. / Homma, M. / Namba, K.
History
DepositionNov 26, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_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: Chemotaxis protein motB
B: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)41,4692
Polymers41,4692
Non-polymers00
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-14 kcal/mol
Surface area16490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.250, 86.400, 129.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chemotaxis protein motB / Motility protein B


Mass: 20734.672 Da / Num. of mol.: 2 / Fragment: C-terminal fragment 2 (UNP residues 99 -276 )
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SJW1103 / Gene: motB / Plasmid: PET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55892
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.1M Tris-HCl, 0.2M Sodium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 35 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2008
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→35.97 Å / Num. all: 36833 / Num. obs: 36833 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.01 / Net I/σ(I): 15.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 5341 / Rsym value: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZOV

2zov


Resolution: 1.75→35.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1558926.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1839 5 %RANDOM
Rwork0.187 ---
obs0.187 36794 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0914 Å2 / ksol: 0.314714 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---3.58 Å20 Å2
3---3.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 0 469 3352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 284 4.7 %
Rwork0.25 5796 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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