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- PDB-4rhr: Crystal structure of PltB -

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Basic information

Entry
Database: PDB / ID: 4rhr
TitleCrystal structure of PltB
ComponentsPutative pertussis-like toxin subunit
KeywordsSUGAR BINDING PROTEIN / sugar binding motif / sugar binding / sugar
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Pertussis-like toxin subunit
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.079 Å
AuthorsGao, X. / Wang, J. / Galan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Host adaptation of a bacterial toxin from the human pathogen salmonella typhi.
Authors: Deng, L. / Song, J. / Gao, X. / Wang, J. / Yu, H. / Chen, X. / Varki, N. / Naito-Matsui, Y. / Galan, J.E. / Varki, A.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pertussis-like toxin subunit
B: Putative pertussis-like toxin subunit
C: Putative pertussis-like toxin subunit
D: Putative pertussis-like toxin subunit
E: Putative pertussis-like toxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4079
Polymers68,1715
Non-polymers2364
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-39 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.091, 97.190, 104.191
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
Putative pertussis-like toxin subunit


Mass: 13634.195 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Gene: STY1891, t1107 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8Z6A3
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 26% (w/v) PEG1500 and 0.1 M sodium acetate, pH5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 23, 2014
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.079→50 Å / Num. obs: 42026 / % possible obs: 99.2 % / Observed criterion σ(F): 1.35
Reflection shellResolution: 2.079→2.15 Å / % possible all: 96.75

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: dev_1701)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.079→30.936 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2099 5.03 %RANDOM
Rwork0.1558 ---
obs0.1576 41691 98.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.079→30.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 16 377 4823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084572
X-RAY DIFFRACTIONf_angle_d1.1576219
X-RAY DIFFRACTIONf_dihedral_angle_d12.3791561
X-RAY DIFFRACTIONf_chiral_restr0.045691
X-RAY DIFFRACTIONf_plane_restr0.006790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.079-2.12740.23111420.17982517X-RAY DIFFRACTION96
2.1274-2.18050.20751560.16812588X-RAY DIFFRACTION99
2.1805-2.23950.24311420.1652610X-RAY DIFFRACTION99
2.2395-2.30540.22841330.16662595X-RAY DIFFRACTION99
2.3054-2.37980.19441390.1682628X-RAY DIFFRACTION99
2.3798-2.46480.2361450.16942613X-RAY DIFFRACTION99
2.4648-2.56340.2041290.17342633X-RAY DIFFRACTION99
2.5634-2.680.25191230.17012633X-RAY DIFFRACTION99
2.68-2.82120.24431260.18822606X-RAY DIFFRACTION97
2.8212-2.99780.21721500.18982545X-RAY DIFFRACTION97
2.9978-3.22910.19561420.16962686X-RAY DIFFRACTION100
3.2291-3.55360.18661440.14972682X-RAY DIFFRACTION100
3.5536-4.06690.16691400.14122694X-RAY DIFFRACTION100
4.0669-5.120.14241540.12082721X-RAY DIFFRACTION100
5.12-30.93910.16831340.14422841X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19740.16960.16611.7962-0.19621.2270.0003-0.0227-0.14250.0055-0.01630.17380.0927-0.06610.02070.1602-0.009-0.00330.1581-0.00570.1863.64417.39359.9402
21.34510.29990.13461.21830.63231.18340.00620.0190.1252-0.06520.01860.1667-0.1027-0.0448-0.01780.19880.0235-0.0080.1565-0.01070.176567.172140.641910.8968
31.89950.5515-0.15092.0403-0.40071.9165-0.0882-0.0813-0.32960.012-0.0351-0.31960.17830.27550.09420.21150.02420.04010.20530.06440.284983.15576.527517.6884
41.71740.5450.23922.0057-0.20261.68960.0262-0.3801-0.1240.2008-0.0876-0.34940.00710.2180.06370.21370.0121-0.01370.34750.05950.300398.92823.018223.4866
52.4716-0.4119-0.45521.82080.22031.2320.0266-0.17750.22420.090.0519-0.1394-0.1430.1903-0.05990.2245-0.01960.02140.2281-0.05680.225189.17744.280819.2471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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