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- PDB-3s0y: The crystal structure of the periplasmic domain of MotB (residues... -

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Basic information

Entry
Database: PDB / ID: 3s0y
TitleThe crystal structure of the periplasmic domain of MotB (residues 64-256).
ComponentsMotility protein B
KeywordsMOTOR PROTEIN / peptidoglycan binding / flagellar rotation / chemotaxis / bacterial flagellar motor / membrane
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / identical protein binding / plasma membrane
Similarity search - Function
Motility protein B-like, N-terminal domain / Membrane MotB of proton-channel complex MotA/MotB / OmpA-like domain / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRoujeinikova, A.R. / O'Neill, J. / Xie, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Role of the MotB linker in the assembly and activation of the bacterial flagellar motor.
Authors: O'Neill, J. / Xie, M. / Hijnen, M. / Roujeinikova, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Cloning, purification and crystallization of MotB, a stator component of the proton-driven bacterial flagellar motor.
Authors: O'Neill, J. / Roujeinikova, A.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Motility protein B
B: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8695
Polymers43,5812
Non-polymers2883
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-57 kcal/mol
Surface area19790 Å2
MethodPISA
2
A: Motility protein B
B: Motility protein B
hetero molecules

A: Motility protein B
B: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,73910
Polymers87,1624
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area13770 Å2
ΔGint-161 kcal/mol
Surface area32690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.210, 75.210, 124.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Motility protein B / Chemotaxis protein MotB


Mass: 21790.582 Da / Num. of mol.: 2 / Fragment: N-terminally truncated (UNP Residues 65-257)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0816, motB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P56427
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.1 M ammonium sulphate, 100 mM MES monohydrate pH 6.5 and 2.5% v/v 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.004 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 30716 / Num. obs: 30716 / % possible obs: 91 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.72 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.177 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1566 5.1 %RANDOM
Rwork0.1779 ---
obs0.1801 30668 90.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.8 Å2 / Biso mean: 34.137 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 15 225 2977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222936
X-RAY DIFFRACTIONr_bond_other_d0.0020.021960
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9664008
X-RAY DIFFRACTIONr_angle_other_deg0.88634830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03225.39141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34315521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2591517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_mcbond_it0.7361.51840
X-RAY DIFFRACTIONr_mcbond_other0.1831.5722
X-RAY DIFFRACTIONr_mcangle_it1.3523015
X-RAY DIFFRACTIONr_scbond_it2.12231096
X-RAY DIFFRACTIONr_scangle_it3.5384.5990
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 102 -
Rwork0.246 2113 -
all-2215 -
obs--90.97 %
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)
13.1668-3.4057-2.75244.14185.00411.44320.68210.35730.5815-0.9918-0.1028-0.6534-1.51850.8652-0.57930.3704-0.0910.16480.21110.04430.1152-1.02850.57364.626
21.25250.3024-0.171.211-0.01851.6156-0.05070.00210.0861-0.07190.06980.1454-0.0974-0.1774-0.01920.04080.0218-0.00620.03670.01170.02037.81839.97922.47
313.4835-3.57274.25171.52750.14454.50050.1213-0.0165-0.57260.06740.231-0.03580.30570.3518-0.35230.0930.0282-0.00670.156-0.13130.247744.10339.45428.31
41.9819-0.2324-0.15511.48890.37521.89520.01820.033-0.2942-0.00130.0682-0.20290.26880.1544-0.08630.08770.04750.00560.0397-0.01450.090224.78924.6421.097
52.0124-0.69890.33312.88091.8011.9861-0.0704-0.0680.292-0.00640.03240.4129-0.0585-0.11730.0380.02280.0122-0.00430.0752-0.03180.083420.18656.57538.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A64 - 89
2X-RAY DIFFRACTION2A93 - 234
3X-RAY DIFFRACTION3A235 - 252
4X-RAY DIFFRACTION4B92 - 234
5X-RAY DIFFRACTION5B235 - 251

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