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- PDB-3gio: Crystal structure of the TNF-alpha inducing protein (Tip alpha) f... -

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Basic information

Entry
Database: PDB / ID: 3gio
TitleCrystal structure of the TNF-alpha inducing protein (Tip alpha) from Helicobacter pylori
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / antiparallel beta sheet / four-helix bundle / loop
Function / homologyHelicobacter TNF-alpha-Inducing protein / Helicobacter TNF-alpha-inducing protein / TNF-alpha-Inducing protein of Helicobacter / Thiol Ester Dehydrase; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / Tumor necrosis factor alpha-inducing protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJang, J.Y. / Yoon, H.J. / Yoon, J.Y. / Kim, H.S. / Lee, S.J. / Kim, K.H. / Kim, D.J. / Han, B.G. / Lee, B.I. / Jang, S. / Suh, S.W.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the TNF-alpha-Inducing Protein (Tipalpha) from Helicobacter pylori: Insights into Its DNA-Binding Activity.
Authors: Jang, J.Y. / Yoon, H.J. / Yoon, J.Y. / Kim, H.S. / Lee, S.J. / Kim, K.H. / Kim, D.J. / Jang, S. / Han, B.G. / Lee, B.I. / Suh, S.W.
History
DepositionMar 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)42,9052
Polymers42,9052
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-9 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.519, 67.114, 91.263
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 uncharacterized protein / Tumor Necrosis Factor alpha inducing protein


Mass: 21452.682 Da / Num. of mol.: 2 / Fragment: UNP residues 28-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0596 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O25318
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl (pH 7.0), 200mM calcium acetate, 20% (w/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A10.97912, 0.97885, 0.96000
SYNCHROTRONPAL/PLS 4A20.96
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 21, 2008
ADSC QUANTUM 2102CCDFeb 20, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.978851
30.961
ReflectionResolution: 2.4→30 Å / Num. obs: 13650 / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 42.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1341 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 714 5.3 %RANDOM
Rwork0.233 ---
all-13147 --
obs-12433 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.662 Å20 Å20 Å2
2---0.251 Å20 Å2
3---10.913 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 70 2460

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