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- PDB-3s0h: The crystal structure of the periplasmic domain of Helicobacter p... -

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Basic information

Entry
Database: PDB / ID: 3s0h
TitleThe crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 90-256).
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: 2.1 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
C: Motility protein B
D: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,52913
Polymers78,6654
Non-polymers8659
Water11,061614
1
A: Motility protein B
D: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6215
Polymers39,3322
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-61 kcal/mol
Surface area16910 Å2
MethodPISA
2
B: Motility protein B
C: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9098
Polymers39,3322
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-98 kcal/mol
Surface area17730 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-187 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.972, 72.972, 127.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Motility protein B / Chemotaxis protein MotB


Mass: 19666.189 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN (UNP Residues 91-257)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: motB, HP_0816 / 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.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.15 Å3/Da / Density % sol: 42.85 %

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Data collection

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: 2.1→51.571 Å / Num. all: 37792 / Num. obs: 37792 / % possible obs: 97.5 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.212.50.3432.21420255810.34398.8
2.21-2.352.60.2552.81344552500.25598.5
2.35-2.512.60.2023.71270549570.20298.4
2.51-2.712.60.14851180645880.14898.1
2.71-2.972.60.1116.51090342030.11197.8
2.97-3.322.60.0937.5989638080.09397.3
3.32-3.832.60.0857.4867833170.08596.8
3.83-4.72.60.0669.3739327920.06696
4.7-6.642.70.0638.7570421470.06394.9
6.64-51.5712.70.0511.4305511490.0592.3

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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: 2.1→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 11.641 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 1903 5 %RANDOM
Rwork0.1813 ---
obs0.1841 37792 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.54 Å2 / Biso mean: 29.618 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 45 614 5846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225553
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9667548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61324.691275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.995151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6521541
X-RAY DIFFRACTIONr_chiral_restr0.0940.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214250
X-RAY DIFFRACTIONr_mcbond_it0.9111.53403
X-RAY DIFFRACTIONr_mcangle_it1.65125573
X-RAY DIFFRACTIONr_scbond_it2.31832150
X-RAY DIFFRACTIONr_scangle_it3.7934.51975
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 134 -
Rwork0.24 2684 -
all-2818 -
obs--98.53 %
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)
10.68290.2340.43460.61460.00660.5831-0.0770.00470.02090.06020.0822-0.0750.01590.0334-0.00530.08270.0062-0.01770.0697-0.01840.0262-10.3481.2797.537
20.2358-0.14110.08371.4904-0.28370.48960.05920.04640.0153-0.0379-0.1029-0.0461-0.0338-0.00450.04370.0658-0.00240.00060.06410.00820.0105-30.09125.535-9.188
30.98670.27660.12021.1011-0.23990.68210.0335-0.0121-0.10180.10230.03230.0990.1736-0.0819-0.06580.1124-0.02530.01010.04310.00480.0289-23.73-10.3856.275
40.4307-0.20350.10851.108-0.16950.68260.0267-0.0045-0.0663-0.1626-0.03050.21840.0704-0.13890.00380.0783-0.0186-0.02750.0697-0.01690.0477-42.9814.441-11.205
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 252
2X-RAY DIFFRACTION2B93 - 252
3X-RAY DIFFRACTION3C84 - 252
4X-RAY DIFFRACTION4D93 - 251

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