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- PDB-3s03: The crystal structure of the periplasmic domain of Helicobacter p... -

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Basic information

Entry
Database: PDB / ID: 3s03
TitleThe crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues 97-256, P43).
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 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)76,17811
Polymers75,5064
Non-polymers6727
Water2,612145
1
A: Motility protein B
D: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9454
Polymers37,7532
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-43 kcal/mol
Surface area15210 Å2
MethodPISA
2
B: Motility protein B
C: Motility protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2337
Polymers37,7532
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-84 kcal/mol
Surface area15100 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-143 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.669, 71.669, 126.236
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: 18876.377 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN (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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 42.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM citric acid pH 5.0, 0.8 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
ReflectionResolution: 2.5→71.67 Å / Num. all: 18607 / Num. obs: 18607 / % possible obs: 85 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.643.40.3192.4955628160.31987.7
2.64-2.83.40.2443.1906226380.24487.2
2.8-2.993.40.1864836224470.18686.5
2.99-3.233.50.1484.7796122830.14886.5
3.23-3.543.50.1275.2723820560.12785.1
3.54-3.953.50.1146659118600.11484.4
3.95-4.563.60.1066.1574616010.10682.8
4.56-5.593.70.0887.5496113560.08882.1
5.59-7.913.70.0778.3382210250.07780.3
7.91-71.6113.80.069.919725250.0674.7

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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→71.67 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.869 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.386 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2843 981 5.3 %RANDOM
Rwork0.2251 ---
obs0.2281 18571 84.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 113.46 Å2 / Biso mean: 50.13 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→71.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 35 145 4664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224593
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9656215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5935556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.88124.825228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63715817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3851529
X-RAY DIFFRACTIONr_chiral_restr0.0760.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213461
X-RAY DIFFRACTIONr_mcbond_it5.5051.52814
X-RAY DIFFRACTIONr_mcangle_it7.40724563
X-RAY DIFFRACTIONr_scbond_it9.16631779
X-RAY DIFFRACTIONr_scangle_it10.8014.51652
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 90 -
Rwork0.38 1327 -
all-1417 -
obs--86.51 %
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)
10.3294-0.03410.05080.25160.07860.0395-0.02110.0386-0.01970.06390.00220.0399-0.00170.01040.0190.14190.0034-0.0070.15130.02850.034110.6770.738-8.96
20.23580.03360.01360.56950.34690.32780.01610.0188-0.05980.015-0.014-0.0274-0.01130.0359-0.0020.12750.0107-0.00750.14810.01070.034821.207-9.741-6.41
30.59630.0177-0.01421.1929-0.4080.1457-0.0669-0.08030.11710.08420.0627-0.0767-0.0009-0.01650.00430.14920.0091-0.07340.0994-0.02810.052331.30825.1228.563
40.8278-0.00240.10610.61150.1450.0575-0.0298-0.00110.01690.0680.0465-0.1301-0.0149-0.0146-0.01670.18830.0049-0.0770.11090.00170.050442.87115.1978.903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A106 - 250
2X-RAY DIFFRACTION2B106 - 251
3X-RAY DIFFRACTION3C106 - 251
4X-RAY DIFFRACTION4D103 - 251

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