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- PDB-3x0u: Crystal structure of PirB -

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Basic information

Entry
Database: PDB / ID: 3x0u
TitleCrystal structure of PirB
ComponentsUncharacterized protein
KeywordsTOXIN / seven-helix bundle / beta barrel / pore-forming toxin
Function / homologyPesticidal crystal protein, N-terminal domain / Delta-Endotoxin; domain 1 / Up-down Bundle / Mainly Alpha / :
Function and homology information
Biological speciesVibrio parahaemolyticus M0605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsWang, H.C. / Ko, T.P. / Wang, A.H.J. / Lo, C.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin.
Authors: Lee, C.T. / Chen, I.T. / Yang, Y.T. / Ko, T.P. / Huang, Y.T. / Huang, J.Y. / Huang, M.F. / Lin, S.J. / Chen, C.Y. / Lin, S.S. / Lin, S.S. / Lightner, D.V. / Wang, H.C. / Wang, A.H. / Wang, H. ...Authors: Lee, C.T. / Chen, I.T. / Yang, Y.T. / Ko, T.P. / Huang, Y.T. / Huang, J.Y. / Huang, M.F. / Lin, S.J. / Chen, C.Y. / Lin, S.S. / Lin, S.S. / Lightner, D.V. / Wang, H.C. / Wang, A.H. / Wang, H.C. / Hor, L.I. / Lo, C.F.
History
DepositionOct 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)102,5162
Polymers102,5162
Non-polymers00
Water17,925995
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)51,2581
Polymers51,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)51,2581
Polymers51,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.897, 128.618, 117.104
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-781-

HOH

21A-887-

HOH

31A-943-

HOH

41A-1016-

HOH

51B-665-

HOH

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Components

#1: Protein Uncharacterized protein / PirB


Mass: 51257.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus M0605 (bacteria)
Gene: AJ90_20625, pirB / Production host: Escherichia coli (E. coli) / References: UniProt: X7RH70
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 995 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20mM Tris, 300mM NaCl, 20% 1,4-butanediol, 0.1M Na-acetate, 15% 2,3-butanediol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 99968 / Num. obs: 99668 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
SHELXSphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.915 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18046 4891 4.9 %RANDOM
Rwork0.14889 ---
all0.15045 100047 --
obs0.15045 94329 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.691 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.1 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 0 995 7849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197027
X-RAY DIFFRACTIONr_bond_other_d0.0010.026404
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9389542
X-RAY DIFFRACTIONr_angle_other_deg0.87314742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20924.974378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.096151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0191530
X-RAY DIFFRACTIONr_chiral_restr0.1110.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021688
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9431.5823382
X-RAY DIFFRACTIONr_mcbond_other1.9421.583381
X-RAY DIFFRACTIONr_mcangle_it3.1062.3584224
X-RAY DIFFRACTIONr_mcangle_other3.1052.364225
X-RAY DIFFRACTIONr_scbond_it2.8511.9153644
X-RAY DIFFRACTIONr_scbond_other2.851.9173645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4652.7595319
X-RAY DIFFRACTIONr_long_range_B_refined7.09314.8379187
X-RAY DIFFRACTIONr_long_range_B_other6.6713.9228660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 346 -
Rwork0.225 6563 -
obs--94.68 %

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