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- PDB-3wpx: Structure of PomBc4, a periplasmic fragment of PomB from Vibrio a... -

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Basic information

Entry
Database: PDB / ID: 3wpx
TitleStructure of PomBc4, a periplasmic fragment of PomB from Vibrio alginolyticus
ComponentsPomB
KeywordsMEMBRANE PROTEIN / ompA-like / stator / peptidoglycan
Function / homology
Function and homology information


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 speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTakao, M. / Sakuma, M. / Zhu, S. / Homma, M. / Kojima, S. / Imada, K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Conformational change in the periplasmic region of the flagellar stator coupled with the assembly around the rotor
Authors: Zhu, S. / Takao, M. / Li, N. / Sakuma, M. / Nishino, Y. / Homma, M. / Kojima, S. / Imada, K.
History
DepositionJan 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Other
Revision 1.3Dec 23, 2015Group: Other
Revision 1.4Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.title
Revision 1.5Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: PomB
B: PomB


Theoretical massNumber of molelcules
Total (without water)45,6932
Polymers45,6932
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-0 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.408, 63.300, 77.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PomB


Mass: 22846.504 Da / Num. of mol.: 2 / Fragment: UNP residues 121-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: pomB / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06874
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.56 Å3/Da / Density % sol: 21.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(w/v) PEGMME2000, 0.1M imidazole, 4%(v/v) MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 16, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→38.6 Å / Num. all: 12786 / Num. obs: 12786 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1876 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BSSdata collection
Cootmodel building
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WPW

3wpw


Resolution: 2.3→32.96 Å / SU ML: 0.63 / σ(F): 1.34 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 1283 10.06 %random
Rwork0.1752 ---
obs0.1812 12759 96.35 %-
all-12786 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.65 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2069 Å20 Å2-0 Å2
2--11.7629 Å20 Å2
3----7.5559 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 0 57 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062437
X-RAY DIFFRACTIONf_angle_d1.013279
X-RAY DIFFRACTIONf_dihedral_angle_d18.219985
X-RAY DIFFRACTIONf_chiral_restr0.064359
X-RAY DIFFRACTIONf_plane_restr0.004444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3001-2.39220.27591420.2094128698
2.3922-2.5010.28461390.2001126098
2.501-2.63280.28141410.1855128798
2.6328-2.79770.24391390.1936126597
2.7977-3.01360.31381490.1994126197
3.0136-3.31660.22261340.1827127696
3.3166-3.79590.21661490.1612125696
3.7959-4.78010.18431370.1496128395
4.7801-32.96330.22951530.1752130292

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