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- PDB-3oss: The crystal structure of enterotoxigenic Escherichia coli GspC-Gs... -

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Basic information

Entry
Database: PDB / ID: 3oss
TitleThe crystal structure of enterotoxigenic Escherichia coli GspC-GspD complex from the type II secretion system
Components
  • TYPE 2 SECRETION SYSTEM, GSPCType II secretion system
  • TYPE 2 SECRETION SYSTEM, SECRETIN GSPDType II secretion system
KeywordsPROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / HR DOMAIN / SECRETIN / LANTHANIDE-BINDING TAG
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / membrane => GO:0016020 / plasma membrane
Similarity search - Function
SH3 type barrels. - #830 / Type II secretion system protein GspC / Bacterial type II secretion system protein C signature. / Type II secretion system protein GspC, N-terminal / Type II secretion system protein C / : / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family ...SH3 type barrels. - #830 / Type II secretion system protein GspC / Bacterial type II secretion system protein C signature. / Type II secretion system protein GspC, N-terminal / Type II secretion system protein C / : / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Ribosomal Protein S8; Chain: A, domain 1 / PDZ superfamily / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Secretin GspD 2 / Type II secretion system protein C 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsKorotkov, K.V. / Pruneda, J. / Hol, W.G.J.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structural and functional studies on the interaction of GspC and GspD in the type II secretion system.
Authors: Korotkov, K.V. / Johnson, T.L. / Jobling, M.G. / Pruneda, J. / Pardon, E. / Heroux, A. / Turley, S. / Steyaert, J. / Holmes, R.K. / Sandkvist, M. / Hol, W.G.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Structure summary
Revision 1.2Nov 2, 2011Group: Database references / Structure summary
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 6, 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_ref_seq_dif / struct_site
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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: TYPE 2 SECRETION SYSTEM, GSPC
D: TYPE 2 SECRETION SYSTEM, SECRETIN GSPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3884
Polymers27,3122
Non-polymers762
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.500, 76.810, 85.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL UNIT IS A DODECAMER, IT IS UNKNOWN AT THE MOMENT HOW INDIVIDUAL SUBUNITS ARE ASSEMBLED IN VIVO

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Components

#1: Protein TYPE 2 SECRETION SYSTEM, GSPC / Type II secretion system


Mass: 7585.665 Da / Num. of mol.: 1 / Fragment: HR DOMAIN, RESIDUES 122-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: H10407 / Gene: GSPC / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3PJ87
#2: Protein TYPE 2 SECRETION SYSTEM, SECRETIN GSPD / Type II secretion system


Mass: 19726.424 Da / Num. of mol.: 1 / Fragment: N0 AND N1 DOMAINS, RESIDUES 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: H10407 / Gene: GSPD / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3PJ86
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA LANTHANIDE BINDING TAG (LBT) WITH THE SEQUENCE YIDTNNDGYIEGDEL WAS INSERTED BETWEEN RESIDUES ...A LANTHANIDE BINDING TAG (LBT) WITH THE SEQUENCE YIDTNNDGYIEGDEL WAS INSERTED BETWEEN RESIDUES MET100 AND VAL113 OF GSPD

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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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.9M MG SULFATE, 0.1M BIS-TRIS PROPANE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 18, 2008
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.63→42.88 Å / Num. all: 17264 / Num. obs: 9399 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.04
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.63-2.70.9032199.8
2.7-2.770.7822.21100
2.77-2.850.662.6199.8
2.85-2.940.4833.5199.9
2.94-3.040.4134199.9
3.04-3.140.3165199.9
3.14-3.260.2995.3199.8
3.26-3.40.27.9199.8
3.4-3.550.1549.41100
3.55-3.720.12111.81100
3.72-3.920.1113.2199.8
3.92-4.160.08316.1199.9
4.16-4.450.06120.71100
4.45-4.80.04824.71100
4.8-5.260.05423.21100
5.26-5.880.06619.51100
5.88-6.790.06319.91100
6.79-8.320.04326.8199.8
8.32-11.760.02741.21100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.48 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å39.15 Å
Translation3 Å39.15 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EZJ

3ezj


Resolution: 2.63→42.88 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 29.319 / SU ML: 0.284 / SU R Cruickshank DPI: 0.5582 / Cross valid method: THROUGHOUT / ESU R: 0.558 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26486 457 4.9 %RANDOM
Rwork0.21261 ---
obs0.2151 8942 99.93 %-
all-9405 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.234 Å2
Baniso -1Baniso -2Baniso -3
1-6.37 Å20 Å20 Å2
2---3.24 Å20 Å2
3----3.13 Å2
Refinement stepCycle: LAST / Resolution: 2.63→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 2 45 1775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221752
X-RAY DIFFRACTIONr_bond_other_d0.0010.021173
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9722364
X-RAY DIFFRACTIONr_angle_other_deg0.81132865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86524.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1481515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4021.51102
X-RAY DIFFRACTIONr_mcbond_other0.0611.5453
X-RAY DIFFRACTIONr_mcangle_it0.80721777
X-RAY DIFFRACTIONr_scbond_it1.3853650
X-RAY DIFFRACTIONr_scangle_it2.5134.5587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 39 -
Rwork0.371 650 -
obs--99.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.52480.895-1.12811.9253-2.94876.79190.0599-0.3147-0.45990.80640.0524-0.06580.0048-0.0183-0.11230.16540.0031-0.07270.1288-0.0030.1034-0.5426-19.987528.4709
26.8326-0.52781.49155.1312-3.08858.0520.276-0.7453-0.32350.9459-0.1608-0.40720.47670.31-0.11520.382-0.0266-0.07050.16860.01070.27266.9874-20.568930.7549
30.8439-1.5798-0.26015.8661.44.90550.06050.0276-0.06850.2459-0.09350.3205-0.1491-0.28390.0330.136-0.0053-0.03380.0825-0.00140.0618-9.0752-7.28420.8481
43.44430.59490.38395.76-1.98688.0758-0.03420.24330.06230.2458-0.0471-0.056-0.04490.0870.08140.05990.0203-0.01890.0489-0.02760.0954-8.4647-7.3998-0.1067
51.33323.1544-2.037631.6126-11.22154.8168-0.0086-0.29780.0863-0.0214-0.177-1.08590.0320.3410.18560.34320.0071-0.03770.3089-0.07460.1745-5.129412.787529.7348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C122 - 150
2X-RAY DIFFRACTION2C151 - 186
3X-RAY DIFFRACTION3D3 - 70
4X-RAY DIFFRACTION3D74 - 80
5X-RAY DIFFRACTION4D99 - 165
6X-RAY DIFFRACTION5D699 - 800

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