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- PDB-3cyp: The crystal structure of the C-terminal domain of Helicobacter py... -

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Basic information

Entry
Database: PDB / ID: 3cyp
TitleThe crystal structure of the C-terminal domain of Helicobacter pylori MotB (residues 125-256).
ComponentsChemotaxis protein motB
KeywordsMEMBRANE PROTEIN / Helicobacter pylori / bacterial flagellar motor / peptidoglycan binding / Bacterial flagellum / Chemotaxis / Flagellar rotation / Inner membrane / Membrane / Transmembrane
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 / Resolution: 1.6 Å
AuthorsRoujeinikova, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: implications for peptidoglycan recognition.
Authors: Roujeinikova, A.
History
DepositionApr 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Chemotaxis protein motB
C: Chemotaxis protein motB
D: Chemotaxis protein motB
E: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)63,7604
Polymers63,7604
Non-polymers00
Water11,007611
1
B: Chemotaxis protein motB
C: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Chemotaxis protein motB
E: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)31,8802
Polymers31,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-24.8 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.816, 89.479, 66.322
Angle α, β, γ (deg.)90.000, 112.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Chemotaxis protein motB / / Motility protein B


Mass: 15939.984 Da / Num. of mol.: 4 / Fragment: C-terminal domain, UNP residues 126-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: motB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P56427
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM Tris/HCl, 16-18% PEG 3350, 200 mM sodium tartrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→61.2 Å / Num. obs: 71913 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.70.3981.939340105550.398100
1.69-1.793.70.2792.73709399140.279100
1.79-1.913.80.1783.93497693100.178100
1.91-2.073.80.125.63289987300.12100
2.07-2.263.80.09273031880240.092100
2.26-2.533.80.0738.72754672600.073100
2.53-2.923.80.0689.22430263890.068100
2.92-3.583.80.069.62074354520.06100
3.58-5.063.70.05311.31575242050.05399.7
5.06-50.573.50.04813.2736220740.04889

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
SHELXSphasing
RefinementResolution: 1.6→50.572 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.932 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3630 5 %RANDOM
Rwork0.185 ---
obs0.188 71888 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.07 Å2
2--0.46 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 0 611 4968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224458
X-RAY DIFFRACTIONr_bond_other_d0.0010.023029
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9456056
X-RAY DIFFRACTIONr_angle_other_deg0.96337388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2824.464233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96915778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.071532
X-RAY DIFFRACTIONr_chiral_restr0.0930.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02916
X-RAY DIFFRACTIONr_nbd_refined0.2280.21078
X-RAY DIFFRACTIONr_nbd_other0.1980.23398
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22256
X-RAY DIFFRACTIONr_nbtor_other0.0880.22333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2453
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.241
X-RAY DIFFRACTIONr_mcbond_it1.4481.53516
X-RAY DIFFRACTIONr_mcbond_other0.2581.51067
X-RAY DIFFRACTIONr_mcangle_it1.57624453
X-RAY DIFFRACTIONr_scbond_it2.54431977
X-RAY DIFFRACTIONr_scangle_it3.6734.51600
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 260 -
Rwork0.239 5071 -
all-5331 -
obs--100 %

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