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- PDB-6ghu: Crystal structure of the periplasmic domain of XcpY, oP crystal form. -

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Basic information

Entry
Database: PDB / ID: 6ghu
TitleCrystal structure of the periplasmic domain of XcpY, oP crystal form.
ComponentsType II secretion system protein L
KeywordsTRANSPORT PROTEIN / ferredoxin fold / dimer / GspL / type II secretion system
Function / homology
Function and homology information


Gram-negative-bacterium-type cell wall / protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Type II secretion system protein GspL / GspL, cytoplasmic actin-ATPase-like domain / GspL periplasmic domain / Type II secretion system (T2SS), protein L / GspL periplasmic domain / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Type II secretion system protein L / Type II secretion system protein L
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFulara, A. / Savvides, S.N.
Funding support1items
OrganizationGrant numberCountry
Research Foundation - Flanders
CitationJournal: Sci Rep / Year: 2018
Title: Structure and oligomerization of the periplasmic domain of GspL from the type II secretion system of Pseudomonas aeruginosa.
Authors: Fulara, A. / Vandenberghe, I. / Read, R.J. / Devreese, B. / Savvides, S.N.
History
DepositionMay 9, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionNov 21, 2018ID: 5N7S
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Type II secretion system protein L
A: Type II secretion system protein L


Theoretical massNumber of molelcules
Total (without water)15,9962
Polymers15,9962
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.395, 64.786, 98.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Type II secretion system protein L / T2SS protein L


Mass: 7998.013 Da / Num. of mol.: 2 / Fragment: periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: xcpY, PAMH19_1972 / Plasmid: pRSF 1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A8RGG2, UniProt: P25060*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M L-Proline, 0.1 M HEPES, pH=7.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2→39.32 Å / Num. obs: 10733 / % possible obs: 99.3 % / Redundancy: 4.05 % / Biso Wilson estimate: 24.29 Å2 / Rrim(I) all: 0.157 / Net I/σ(I): 7.42
Reflection shellResolution: 2→2.2 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w7v

2w7v


Resolution: 2→39.32 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.08
RfactorNum. reflection% reflection
Rfree0.2692 1066 9.97 %
Rwork0.2217 --
obs0.2265 10691 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.69 Å2 / Biso mean: 32.9993 Å2 / Biso min: 14.4 Å2
Refinement stepCycle: final / Resolution: 2→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 0 97 1209
Biso mean---34.73 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041188
X-RAY DIFFRACTIONf_angle_d0.6811617
X-RAY DIFFRACTIONf_chiral_restr0.047195
X-RAY DIFFRACTIONf_plane_restr0.005219
X-RAY DIFFRACTIONf_dihedral_angle_d18.43723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9998-2.09090.36071300.31621173130398
2.0909-2.20110.30871290.271711691298100
2.2011-2.3390.28231340.23111196133099
2.339-2.51950.33041300.22431171130199
2.5195-2.7730.26321320.23161191132399
2.773-3.17410.31181340.216912151349100
3.1741-3.99850.23461350.19441232136799
3.9985-39.32790.22841420.20561278142097

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