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- PDB-3s02: The crystal structure of the periplasmic domain of Helicobacter p... -

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Basic information

Entry
Database: PDB / ID: 3s02
TitleThe crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 103-256)
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: 2.5 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 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Motility protein B
B: Motility protein B


Theoretical massNumber of molelcules
Total (without water)35,2062
Polymers35,2062
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-7 kcal/mol
Surface area16540 Å2
MethodPISA
2
A: Motility protein B
B: Motility protein B

A: Motility protein B
B: Motility protein B


Theoretical massNumber of molelcules
Total (without water)70,4124
Polymers70,4124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area10760 Å2
ΔGint-55 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.803, 75.803, 140.811
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Motility protein B / Chemotaxis protein MotB


Mass: 17602.895 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP Residues 104-257)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH 6.5, 6% PEG 20k, 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: 2.5→65.65 Å / Num. all: 16788 / Num. obs: 16761 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 14.5
Reflection shell
Num. measured allDiffraction-ID
109211
103971
96231
90261
82281
75251
62861
52481
45241
24521

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Processing

Software
NameVersionClassificationNB
SCALA3.3.1data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→65.65 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.099 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 851 5.1 %RANDOM
Rwork0.181 ---
obs0.184 15909 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.32 Å2 / Biso mean: 24.237 Å2 / Biso min: 2.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→65.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 0 153 2511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222428
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9573289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66624.919124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45215440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4511516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211852
X-RAY DIFFRACTIONr_mcbond_it0.8261.51487
X-RAY DIFFRACTIONr_mcangle_it1.67722427
X-RAY DIFFRACTIONr_scbond_it2.5843941
X-RAY DIFFRACTIONr_scangle_it4.4924.5862
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 64 -
Rwork0.214 1118 -
all-1182 -
obs--100 %
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)
10.5208-0.1171-0.23410.0884-0.08050.39760.02240.0008-0.0217-0.00010.00550.022-0.0282-0.033-0.02790.0351-0.0035-0.00060.0491-0.00470.029642.492-19.7135.573
20.5467-0.23650.43720.1944-0.16430.6737-0.00190.0132-0.0431-0.01060.00960.0314-0.0261-0.0619-0.00770.0252-0.00550.01270.0357-0.00120.027943.614-20.588-9.144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A107 - 251
2X-RAY DIFFRACTION2B107 - 252

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