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- PDB-3x0t: Crystal structure of PirA -

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Basic information

Entry
Database: PDB / ID: 3x0t
TitleCrystal structure of PirA
ComponentsUncharacterized protein
KeywordsTOXIN / Jelly roll fold / pore forming toxin
Function / homologyNITRATE ION / :
Function and homology information
Biological speciesVibrio parahaemolyticus M0605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.17 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 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8928
Polymers27,5202
Non-polymers3726
Water9,386521
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8222
Polymers13,7601
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0706
Polymers13,7601
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.397, 67.338, 53.669
Angle α, β, γ (deg.)90.00, 122.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-505-

HOH

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Components

#1: Protein Uncharacterized protein / PirA


Mass: 13760.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus M0605 (bacteria)
Gene: AJ90_20630, pirA / Production host: Escherichia coli (E. coli) / References: UniProt: X7REN0
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 30mM Tris HCl, 100mM NaCl, 1mM DTT, 5% glycerol, 20% PEG 3350, 0.2M KNO3, 15% ethylene glycol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. all: 78940 / Num. obs: 78388 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 33.8
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.17→47.1 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.962 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16926 3862 4.9 %RANDOM
Rwork0.1308 ---
all0.13275 78862 --
obs0.13275 74525 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.512 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.36 Å2
2--0.35 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.17→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 24 521 2328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4651.9042674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3224.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.25315302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8631513
X-RAY DIFFRACTIONr_chiral_restr0.1470.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211591
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.9561.51158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.84921867
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.2063797
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.1264.5797
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.14331955
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.169→1.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 281 -
Rwork0.235 5237 -
obs--94.58 %

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