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- PDB-5vtm: The crystal structure of minor pseudopilin ternary complex of Xcp... -

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Basic information

Entry
Database: PDB / ID: 5vtm
TitleThe crystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2 secretion system of Pseudomonas aeruginosa
Components
  • Type II secretion system protein I
  • Type II secretion system protein J
  • Type II secretion system protein K
KeywordsTRANSPORT PROTEIN / Type 2 secretion system
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / plasma membrane
Similarity search - Function
General secretion pathway protein K / GspK, central domain superfamily / : / : / Type II secretion system (T2SS), protein K / Type II secretion system (T2SS), protein K / Type II secretion system protein GspI, C-terminal / Type II secretion system protein GspI / Type II secretion system (T2SS), protein I / Type II secretion system protein GspJ ...General secretion pathway protein K / GspK, central domain superfamily / : / : / Type II secretion system (T2SS), protein K / Type II secretion system (T2SS), protein K / Type II secretion system protein GspI, C-terminal / Type II secretion system protein GspI / Type II secretion system (T2SS), protein I / Type II secretion system protein GspJ / Type II secretion system (T2SS), protein J / GSPII I/J protein-like / : / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system protein I / Type II secretion system protein J / Type II secretion system protein K
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.041 Å
AuthorsZhang, Y. / Jia, Z.
CitationJournal: PLoS Pathog. / Year: 2018
Title: Structure-guided disruption of the pseudopilus tip complex inhibits the Type II secretion in Pseudomonas aeruginosa.
Authors: Zhang, Y. / Faucher, F. / Zhang, W. / Wang, S. / Neville, N. / Poole, K. / Zheng, J. / Jia, Z.
History
DepositionMay 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: Type II secretion system protein J
X: Type II secretion system protein K
V: Type II secretion system protein I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5626
Polymers63,4423
Non-polymers1203
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-36 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.546, 76.760, 102.861
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 Type II secretion system protein J / T2SS protein J / General secretion pathway protein J / PilD-dependent protein PddD


Mass: 22247.691 Da / Num. of mol.: 1 / Fragment: residues 44-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpW, pddD, PA3098 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00517
#2: Protein Type II secretion system protein K / T2SS protein K / General secretion pathway protein K


Mass: 30659.467 Da / Num. of mol.: 1 / Fragment: residues 44-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpX, PA3097 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00518
#3: Protein Type II secretion system protein I / T2SS protein I / General secretion pathway protein I / PilD-dependent protein PddC


Mass: 10534.801 Da / Num. of mol.: 1 / Fragment: residues 38-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: xcpV, pddC, PA3099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00516
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 35.81 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 19 %-22 % PEG 2000 MME, 0.1M Tris, pH 8.0-9.0, 0.2 M trimethylamine N-oxide
PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→43.51 Å / Num. obs: 31625 / % possible obs: 99.2 % / Redundancy: 9.8 % / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Net I/σ(I): 10.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BW0, 3CI0

5bw0

3ci0


Resolution: 2.041→43.51 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2481 2000 6.32 %
Rwork0.1909 --
obs0.1945 31625 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.041→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4049 0 3 288 4340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084120
X-RAY DIFFRACTIONf_angle_d0.9155553
X-RAY DIFFRACTIONf_dihedral_angle_d9.2922506
X-RAY DIFFRACTIONf_chiral_restr0.052590
X-RAY DIFFRACTIONf_plane_restr0.005736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0412-2.09220.26231410.19032089X-RAY DIFFRACTION100
2.0922-2.14880.27691400.1942073X-RAY DIFFRACTION100
2.1488-2.2120.27811400.18972080X-RAY DIFFRACTION100
2.212-2.28340.25211420.19572098X-RAY DIFFRACTION100
2.2834-2.3650.26551410.20182088X-RAY DIFFRACTION100
2.365-2.45970.26951430.19052111X-RAY DIFFRACTION100
2.4597-2.57160.26361400.20622093X-RAY DIFFRACTION100
2.5716-2.70720.27641420.20542094X-RAY DIFFRACTION100
2.7072-2.87680.27841410.21332088X-RAY DIFFRACTION100
2.8768-3.09880.25411450.19222133X-RAY DIFFRACTION100
3.0988-3.41060.23821430.18482133X-RAY DIFFRACTION100
3.4106-3.90380.24111440.18032132X-RAY DIFFRACTION100
3.9038-4.91730.21051440.17142143X-RAY DIFFRACTION98
4.9173-43.51980.2411540.20012270X-RAY DIFFRACTION100

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