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- PDB-9gtx: Structural and functional analysis of the Helicobacter pylori lip... -

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Basic information

Entry
Database: PDB / ID: 9gtx
TitleStructural and functional analysis of the Helicobacter pylori lipoprotein chaperone LolA
ComponentsOuter-membrane lipoprotein carrier protein
KeywordsTRANSPORT PROTEIN / Lipoprotein / transport / protein transport
Function / homologyOuter membrane lipoprotein carrier protein LolA, Proteobacteria / Outer membrane lipoprotein carrier protein LolA / Outer membrane lipoprotein carrier protein LolA-like / Lipoprotein localisation LolA/LolB/LppX / lipoprotein localization to outer membrane / lipoprotein transport / outer membrane-bounded periplasmic space / DI(HYDROXYETHYL)ETHER / Outer-membrane lipoprotein carrier protein
Function and homology information
Biological speciesHelicobacter pylori J99 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJaiman, D. / Persson, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Kempe FoundationJCSMK23-0215 Sweden
CitationJournal: Front Microbiol / Year: 2024
Title: Structural and functional analysis of the Helicobacter pylori lipoprotein chaperone LolA.
Authors: Jaiman, D. / Persson, K.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer-membrane lipoprotein carrier protein
B: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1774
Polymers38,9652
Non-polymers2122
Water1,964109
1
A: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5892
Polymers19,4831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer-membrane lipoprotein carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5892
Polymers19,4831
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.749, 65.461, 60.807
Angle α, β, γ (deg.)90.000, 99.237, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Outer-membrane lipoprotein carrier protein


Mass: 19482.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The signal peptide of the protein is not included in the construct. The first methionine in this construct originates from an expression tag that was cleaved off with TEV protease.
Source: (gene. exp.) Helicobacter pylori J99 (bacteria) / Gene: lolA, jhp_0722 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZL58
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 50% pentaerythriol propoxylate 0.1 M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.04→44.24 Å / Num. obs: 20710 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.059 / Rrim(I) all: 0.154 / Χ2: 0.83 / Net I/σ(I): 9.2 / Num. measured all: 142035
Reflection shellResolution: 2.04→2.11 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.113 / Num. measured all: 14420 / Num. unique obs: 2017 / CC1/2: 0.494 / Rpim(I) all: 0.447 / Rrim(I) all: 1.2 / Χ2: 0.77 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1.5286refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→44.24 Å / SU ML: 0.2936 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2514 1035 5 %
Rwork0.2002 19658 -
obs0.2029 20693 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.14 Å2
Refinement stepCycle: LAST / Resolution: 2.04→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2654 0 14 109 2777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752728
X-RAY DIFFRACTIONf_angle_d0.86853682
X-RAY DIFFRACTIONf_chiral_restr0.0561411
X-RAY DIFFRACTIONf_plane_restr0.0056463
X-RAY DIFFRACTIONf_dihedral_angle_d23.26311044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.150.34431460.28752775X-RAY DIFFRACTION100
2.15-2.280.36061470.25292800X-RAY DIFFRACTION100
2.28-2.460.29391490.25142816X-RAY DIFFRACTION99.97
2.46-2.710.25411470.2112786X-RAY DIFFRACTION99.97
2.71-3.10.28791460.20782794X-RAY DIFFRACTION100
3.1-3.90.23931490.19182825X-RAY DIFFRACTION100
3.9-44.240.20931510.17122862X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: -10.547166721774 Å / Origin y: -1.8438590596441 Å / Origin z: 39.474332193951 Å
111213212223313233
T0.21190774161269 Å2-0.036525267508955 Å2-0.039022854169172 Å2-0.27194462858083 Å20.0094525911256221 Å2--0.32339189450386 Å2
L1.1611839079543 °2-0.09346126309622 °2-0.29496897612814 °2-0.70242757464047 °2-0.12187491794958 °2--1.2371096284178 °2
S0.099503027457013 Å °-0.14252063492675 Å °-0.05592363262701 Å °0.099587336573804 Å °-0.050310837932096 Å °-0.070407740103446 Å °-0.031575083398412 Å °-0.021989915609023 Å °-0.059465305090753 Å °
Refinement TLS groupSelection details: all

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