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- PDB-2zov: Structure of the periplasmic domain of MotB from Salmonella (crys... -

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Basic information

Entry
Database: PDB / ID: 2zov
TitleStructure of the periplasmic domain of MotB from Salmonella (crystal form I)
ComponentsChemotaxis protein motB
KeywordsMEMBRANE PROTEIN / 2-layer sandwich / Bacterial flagellum / Cell projection / Chemotaxis / Flagellar rotation / Inner membrane / Membrane / Transmembrane
Function / homology
Function and homology information


archaeal or bacterial-type flagellum-dependent cell motility / chemotaxis / 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 speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsImada, K. / Kojima, S. / Namba, K. / Homma, M.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Stator assembly and activation mechanism of the flagellar motor by the periplasmic region of MotB
Authors: Kojima, S. / Imada, K. / Sakuma, M. / Sudo, Y. / Kojima, C. / Minamino, T. / Homma, M. / Namba, K.
History
DepositionJun 9, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)23,9821
Polymers23,9821
Non-polymers00
Water3,675204
1
A: Chemotaxis protein motB

A: Chemotaxis protein motB


Theoretical massNumber of molelcules
Total (without water)47,9642
Polymers47,9642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2960 Å2
ΔGint2 kcal/mol
Surface area15910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.740, 99.740, 43.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chemotaxis protein motB / Motility protein B


Mass: 23982.191 Da / Num. of mol.: 1 / Fragment: C-terminal fragment 1, UNP Residues 88-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: P55892
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 6% PEG 4000, 0.1M Acetate, 0.22M Zn(OAc)2, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979101,0.979397,0.9730,0.9860
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008
RadiationMonochromator: double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791011
20.9793971
30.9731
40.9861
ReflectionResolution: 2→33 Å / Num. all: 17248 / Num. obs: 17162 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 22.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 8 / Num. unique all: 2473 / Rsym value: 0.26 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→32.65 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1429599.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 866 5.1 %RANDOM
Rwork0.233 ---
obs0.233 17140 99.2 %-
all-17278 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.913 Å2 / ksol: 0.336106 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å22.08 Å20 Å2
2---0.65 Å20 Å2
3---1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 0 204 1508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.832
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 142 5.1 %
Rwork0.251 2669 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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