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- PDB-3vnc: Crystal Structure of TIP-alpha N25 from Helicobacter Pylori in it... -

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Basic information

Entry
Database: PDB / ID: 3vnc
TitleCrystal Structure of TIP-alpha N25 from Helicobacter Pylori in its natural dimeric form
ComponentsTIP-alpha
KeywordsDNA BINDING PROTEIN / TNF-alpha-inducing Protein / HP0596 / Homodimer / Carcinogenic Factor
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: 2.6 Å
AuthorsGao, M. / Li, D. / Hu, Y. / Zou, Q. / Wang, D.-C.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of TNF-alpha-Inducing Protein from Helicobacter Pylori in Active Form Reveals the Intrinsic Molecular Flexibility for Unique DNA-Binding
Authors: Gao, M. / Li, D. / Hu, Y. / Zhang, Y. / Zou, Q. / Wang, D.-C.
History
DepositionJan 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TIP-alpha
B: TIP-alpha


Theoretical massNumber of molelcules
Total (without water)38,4462
Polymers38,4462
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-2 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.700, 46.936, 99.100
Angle α, β, γ (deg.)90.00, 127.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TIP-alpha / Putative uncharacterized protein


Mass: 19223.031 Da / Num. of mol.: 2 / Fragment: Residues 25-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0596 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3) / References: UniProt: O25318
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 16% PEG3350, 80% Tacsimate, 2% 1,2-propanediol, 5% MPD, 5% Glycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97898, 0.97917, 0.96395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2009
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979171
30.963951
ReflectionResolution: 2.6→49.14 Å / Num. all: 15779 / Num. obs: 15054 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2289 / Rsym value: 0.374 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→49.14 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2045408.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1527 10.1 %RANDOM
Rwork0.231 ---
obs0.231 15054 95.1 %-
all-15815 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.6298 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.88 Å20 Å211.46 Å2
2---16.65 Å20 Å2
3---3.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 0 55 2437
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 209 9.4 %
Rwork0.319 2013 -
obs-2289 85.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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