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- PDB-3s06: The crystal structure of the periplasmic domain of Helicobacter p... -

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Basic information

Entry
Database: PDB / ID: 3s06
TitleThe crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 97-256, P3121).
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.
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: To be published
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)37,8493
Polymers37,7532
Non-polymers961
Water7,260403
1
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)75,6986
Polymers75,5064
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area10740 Å2
ΔGint-75 kcal/mol
Surface area28210 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-16 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.714, 70.714, 143.421
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-87-

HOH

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Components

#1: Protein Motility protein B / Chemotaxis protein MotB


Mass: 18876.377 Da / Num. of mol.: 2 / Fragment: C-terminal fragment (UNP residues 98-257)
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.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 100 mM Bicine pH 9.0, 2 M Ammonium Sulphate , 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
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 7.6 / Number: 214679 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / D res high: 1.7 Å / D res low: 56.344 Å / Num. obs: 38287 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6956.3493.610.0270.0275.3
4.025.6996.110.040.045.6
3.294.0296.910.0530.0535.7
2.853.2997.310.0630.0635.7
2.552.859810.0630.0635.7
2.322.5598.310.080.085.6
2.152.3298.610.1040.1045.6
2.012.1598.810.1410.1415.6
1.92.019910.2050.2055.6
1.81.999.210.3290.3295.6
ReflectionResolution: 1.8→61.24 Å / Num. all: 38287 / Num. obs: 38287 / % possible obs: 98.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.701 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1916 5 %RANDOM
Rwork0.17 ---
obs0.1718 38287 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.16 Å2 / Biso mean: 15.9676 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 5 403 2877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222818
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.963863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49324.748139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5215518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3241520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212217
X-RAY DIFFRACTIONr_mcbond_it0.7091.51737
X-RAY DIFFRACTIONr_mcangle_it1.34422875
X-RAY DIFFRACTIONr_scbond_it2.28531081
X-RAY DIFFRACTIONr_scangle_it3.8524.5979
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 155 -
Rwork0.222 2652 -
all-2807 -
obs--99.01 %
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)
10.16530.0940.21550.61830.3380.9298-0.0132-0.0098-0.046-0.04410.0293-0.0264-0.03970.0028-0.01610.0148-0.00140.0060.04060.00070.0222-30.55116.727-36.771
20.9650.2090.51430.4653-0.1950.7209-0.00790.0953-0.047-0.01730.04180.04030.00470.0037-0.03390.03240.0071-0.00970.0433-0.01250.0146-31.80417.853-53.257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 252
2X-RAY DIFFRACTION2B105 - 250

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