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- PDB-5n7l: Crystal structure of the periplasmic domain of XcpY, tI crystal form. -

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Basic information

Entry
Database: PDB / ID: 5n7l
TitleCrystal structure of the periplasmic domain of XcpY, tI crystal form.
ComponentsType II secretion system protein LType II secretion system
KeywordsPROTEIN TRANSPORT / periplasm / ferrodoxin fold / GspL protein
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 / 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
BROMIDE ION / GLUTAMIC ACID / Type II secretion system protein L
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å
AuthorsFulara, A. / Savvides, S.N.
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
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 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
A: Type II secretion system protein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7937
Polymers8,1121
Non-polymers6816
Water21612
1
A: Type II secretion system protein L
hetero molecules

A: Type II secretion system protein L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,58614
Polymers16,2242
Non-polymers1,36212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+1/2,y,-z-1/41
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.439, 100.439, 98.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-403-

BR

21A-509-

HOH

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Components

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


Mass: 8112.118 Da / Num. of mol.: 1 / Fragment: periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: xcpY, PA3096 / Plasmid: pRSF 1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25060
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Fragment: Glu- side chains / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 6.23 Å3/Da / Density % sol: 80.25 % / Description: bipiramide
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3 M KBr or 0.2 M MgCl2, 0.1 M sodium cacodylate, pH=6.5, gamma-PGA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→41 Å / Num. obs: 9039 / % possible obs: 99.7 % / Redundancy: 12.97 % / Rrim(I) all: 0.13 / Net I/σ(I): 16.56
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 12.02 % / Num. unique obs: 1419 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1model building
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7S

5n7s
PDB Unreleased entry


Resolution: 2.501→40.894 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 902 10 %random
Rwork0.2012 ---
obs0.2031 9018 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.83 Å2 / Biso mean: 75.5813 Å2 / Biso min: 39.5 Å2
Refinement stepCycle: final / Resolution: 2.501→40.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 0 19 12 600
Biso mean--105.04 65.58 -
Num. residues----80
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004611
X-RAY DIFFRACTIONf_angle_d0.805825
X-RAY DIFFRACTIONf_chiral_restr0.04799
X-RAY DIFFRACTIONf_plane_restr0.005112
X-RAY DIFFRACTIONf_dihedral_angle_d2.159483
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5006-2.65730.36031430.34491300144398
2.6573-2.86240.32381480.299413301478100
2.8624-3.15030.26831500.261513421492100
3.1503-3.6060.24541490.196713481497100
3.606-4.54220.19791520.168813571509100
4.5422-40.89910.18011600.176914391599100
Refinement TLS params.Method: refined / Origin x: 15.5543 Å / Origin y: -0.0021 Å / Origin z: -5.7139 Å
111213212223313233
T0.4193 Å2-0.0164 Å20.0707 Å2-0.6027 Å2-0.0253 Å2--0.5363 Å2
L0.8072 °20.7396 °20.0282 °2-0.7923 °20.4283 °2--1.4559 °2
S0.0411 Å °0.3037 Å °0.1642 Å °-0.114 Å °0.1767 Å °-0.1697 Å °-0.0538 Å °0.299 Å °0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 3
2X-RAY DIFFRACTION1allA303 - 382
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allC2 - 3
5X-RAY DIFFRACTION1allS1 - 7
6X-RAY DIFFRACTION1allS8
7X-RAY DIFFRACTION1allS9 - 12

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