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- PDB-2wcq: Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pyl... -

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Basic information

Entry
Database: PDB / ID: 2wcq
TitleCrystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pylori at pH4
ComponentsTNF-ALPHA INDUCER PROTEIN
KeywordsIMMUNE SYSTEM / HP0596 / TIP-ALPHA / HELICOBACTER PYLORI
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 / CITRIC ACID / Tumor necrosis factor alpha-inducing protein
Function and homology information
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTosi, T. / Cioci, G. / Jouravleva, K. / Dian, C. / Terradot, L.
CitationJournal: FEBS Lett. / Year: 2009
Title: Structures of the Tumor Necrosis Factor Alpha Inducing Protein Tipalpha: A Novel Virulence Factor from Helicobacter Pylori.
Authors: Tosi, T. / Cioci, G. / Jouravleva, K. / Dian, C. / Terradot, L.
History
DepositionMar 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF-ALPHA INDUCER PROTEIN
B: TNF-ALPHA INDUCER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8464
Polymers36,4622
Non-polymers3842
Water2,324129
1
A: TNF-ALPHA INDUCER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4232
Polymers18,2311
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TNF-ALPHA INDUCER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4232
Polymers18,2311
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)31.360, 101.990, 47.255
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TNF-ALPHA INDUCER PROTEIN


Mass: 18230.916 Da / Num. of mol.: 2 / Fragment: FRAGMENT AFTER TRYPSIN DIGESTION, RESIDUES 34-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET151-D TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25318
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 4 / Details: 100 MM CITRATE PH 4, 18% PEG 4000, 15 MM ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.8→50.96 Å / Num. obs: 22965 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.08 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.62
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.23 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→47.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.51 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1180 5.1 %RANDOM
Rwork0.195 ---
obs0.197 21752 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.13 Å2
2--0.59 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 26 129 2449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222350
X-RAY DIFFRACTIONr_bond_other_d0.0050.021554
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9633175
X-RAY DIFFRACTIONr_angle_other_deg0.9133804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6624.811106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48215421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6831514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
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_it0.9841.51458
X-RAY DIFFRACTIONr_mcbond_other0.2331.5590
X-RAY DIFFRACTIONr_mcangle_it1.85522349
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9023892
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9074.5826
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 81 -
Rwork0.277 1377 -
obs--83.51 %

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