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- PDB-3s0w: The crystal structure of the periplasmic domain of Helicobacter p... -

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Basic information

Entry
Database: PDB / ID: 3s0w
TitleThe crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 78-256).
ComponentsMotility protein B
KeywordsMOTOR PROTEIN / peptidoglycan binding / flagellar rotation / chemotaxis / bacterial flagellar motor / membrane
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent cell motility / chemotaxis / identical protein binding
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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoujeinikova, A.R.
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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Motility protein B
B: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1735
Polymers41,8852
Non-polymers2883
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-55 kcal/mol
Surface area16970 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)84,34710
Polymers83,7704
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area13140 Å2
ΔGint-157 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.704, 74.704, 126.507
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: 20942.543 Da / Num. of mol.: 2 / Fragment: C-terminal fragment (UNP Residues 79-257)
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.: 89 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 2.5 M AS , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→64.282 Å / Num. all: 12864 / Num. obs: 12864 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.645.70.3332.31024818110.33399
2.64-2.85.60.243.2987617500.2499.3
2.8-2.995.60.1674.6924516390.16799.3
2.99-3.235.60.1097855815200.10999.3
3.23-3.545.60.0769.6791214200.07699.5
3.54-3.955.50.05911.7722313070.05999.6
3.95-4.565.50.05212631911550.05299.6
4.56-5.595.40.03716.853529920.03799.5
5.59-7.915.20.03516.341317990.03599.8
7.91-64.2824.70.02423.522104710.02497.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.1data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 20.11 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.726 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 624 4.9 %RANDOM
Rwork0.1932 ---
obs0.1959 12850 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.21 Å2 / Biso mean: 46.019 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 15 89 2608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222705
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.963679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71524.667135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17515486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4151520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212086
X-RAY DIFFRACTIONr_mcbond_it0.8261.51668
X-RAY DIFFRACTIONr_mcangle_it1.57422728
X-RAY DIFFRACTIONr_scbond_it2.15931037
X-RAY DIFFRACTIONr_scangle_it3.6844.5951
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 40 -
Rwork0.232 874 -
all-914 -
obs--98.81 %
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)
12.79980.47220.41041.70830.05091.1026-0.2615-0.00310.1683-0.08270.22680.16410.0373-0.18490.03470.20390.03380.01270.1592-0.00210.046112.10939.85923.753
22.63380.7791-0.41821.77560.75291.4355-0.26610.0635-0.59140.01320.2638-0.51230.35180.08610.00230.2410.05560.06390.1444-0.06050.220824.09427.78823.158
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A93 - 251
2X-RAY DIFFRACTION2B94 - 251

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