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- PDB-5ok8: Crystal structure of protein Lpp20 (HP1456) from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5ok8
TitleCrystal structure of protein Lpp20 (HP1456) from Helicobacter pylori
ComponentsLPP20 lipoprotein
KeywordsUNKNOWN FUNCTION / Virulence factor / Helicobacter pylori / Lipoprotein
Function / homologyLipoprotein LPP20 / Lipoprotein LPP20-like / LPP20 lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / LPP20 lipoprotein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.874 Å
AuthorsZanotti, G. / Mishra, N. / Valesse, F.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Helicobacter pylori antigenic Lpp20 is a structural homologue of Tip alpha and promotes epithelial-mesenchymal transition.
Authors: Vallese, F. / Mishra, N.M. / Pagliari, M. / Berto, P. / Codolo, G. / de Bernard, M. / Zanotti, G.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPP20 lipoprotein
B: LPP20 lipoprotein
C: LPP20 lipoprotein
D: LPP20 lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8396
Polymers76,5614
Non-polymers2782
Water6,612367
1
A: LPP20 lipoprotein


Theoretical massNumber of molelcules
Total (without water)19,1401
Polymers19,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LPP20 lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4193
Polymers19,1401
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LPP20 lipoprotein


Theoretical massNumber of molelcules
Total (without water)19,1401
Polymers19,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LPP20 lipoprotein


Theoretical massNumber of molelcules
Total (without water)19,1401
Polymers19,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.303, 90.424, 114.522
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
LPP20 lipoprotein


Mass: 19140.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain J99 / ATCC 700824) (bacteria)
Gene: lpp20, jhp_1349
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A0V1
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.83 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M CaCl2, 0.1 M HEPES (pH 7.5), 20% PEG 6000 (solution number 44 of PEGS-II Suit screen, Quiagen, Germany)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.86→48.38 Å / Num. obs: 87448 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.018 / Net I/σ(I): 21
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.992 / Rpim(I) all: 0.471 / % possible all: 89.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.874→48.377 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 4374 5 %
Rwork0.2289 --
obs0.2308 87448 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.874→48.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 16 367 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083606
X-RAY DIFFRACTIONf_angle_d1.0254850
X-RAY DIFFRACTIONf_dihedral_angle_d16.0022227
X-RAY DIFFRACTIONf_chiral_restr0.073570
X-RAY DIFFRACTIONf_plane_restr0.005617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8741-1.89540.017390.0186807X-RAY DIFFRACTION37
1.8954-1.91770.5921050.52211935X-RAY DIFFRACTION97
1.9177-1.9410.58291520.48072904X-RAY DIFFRACTION100
1.941-1.96560.68131460.55722849X-RAY DIFFRACTION98
1.9656-1.99150.35841540.32362891X-RAY DIFFRACTION100
1.9915-2.01880.31491520.30392823X-RAY DIFFRACTION100
2.0188-2.04760.30211540.28972890X-RAY DIFFRACTION100
2.0476-2.07820.28021530.2662887X-RAY DIFFRACTION100
2.0782-2.11060.2881500.26742853X-RAY DIFFRACTION100
2.1106-2.14520.30431500.26892890X-RAY DIFFRACTION100
2.1452-2.18220.30171550.26572844X-RAY DIFFRACTION100
2.1822-2.22190.27891520.30272863X-RAY DIFFRACTION99
2.2219-2.26470.40481520.34242889X-RAY DIFFRACTION99
2.2647-2.31090.28421450.3042829X-RAY DIFFRACTION98
2.3109-2.36110.29661490.26432859X-RAY DIFFRACTION100
2.3611-2.41610.29771520.24922896X-RAY DIFFRACTION100
2.4161-2.47650.30861510.24082859X-RAY DIFFRACTION100
2.4765-2.54340.35561500.25772896X-RAY DIFFRACTION99
2.5434-2.61830.32841480.23972857X-RAY DIFFRACTION100
2.6183-2.70280.25941510.24672894X-RAY DIFFRACTION100
2.7028-2.79940.25481520.23542886X-RAY DIFFRACTION100
2.7994-2.91140.25481540.24322886X-RAY DIFFRACTION100
2.9114-3.04390.28141500.25092848X-RAY DIFFRACTION100
3.0439-3.20440.2941540.23722880X-RAY DIFFRACTION100
3.2044-3.40510.2891480.22112885X-RAY DIFFRACTION100
3.4051-3.66790.24431560.19892865X-RAY DIFFRACTION99
3.6679-4.03680.20431510.18392824X-RAY DIFFRACTION99
4.0368-4.62060.19981460.17192862X-RAY DIFFRACTION99
4.6206-5.81990.21891530.19132837X-RAY DIFFRACTION99
5.8199-48.39310.24031500.19192886X-RAY DIFFRACTION100

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