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- PDB-3g20: Crystal structure of the major pseudopilin from the type 2 secret... -

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Basic information

Entry
Database: PDB / ID: 3g20
TitleCrystal structure of the major pseudopilin from the type 2 secretion system of enterohaemorrhagic Escherichia coli
ComponentsType II secretion proteinType II secretion system
KeywordsPROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / MAJOR PILIN / COMPLEX
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Type II secretion system protein GspG / Type II secretion system protein GspG, C-terminal / Type II secretion system (T2SS), protein G / Glycoprotein, Type 4 Pilin / Bacterial general secretion pathway protein G-type pilin / Glycoprotein, Type 4 Pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system core protein G
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsKorotkov, K.V. / Gray, M.D. / Kreger, A. / Turley, S. / Sandkvist, M. / Hol, W.G.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Calcium is essential for the major pseudopilin in the type 2 secretion system.
Authors: Korotkov, K.V. / Gray, M.D. / Kreger, A. / Turley, S. / Sandkvist, M. / Hol, W.G.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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
A: Type II secretion protein
B: Type II secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,12210
Polymers27,4662
Non-polymers6568
Water4,792266
1
A: Type II secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0044
Polymers13,7331
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type II secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1196
Polymers13,7331
Non-polymers3855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.120, 36.830, 61.270
Angle α, β, γ (deg.)106.940, 99.050, 90.170
Int Tables number1
Space group name H-MP1
DetailsTHIS CRYSTAL FORM CONTAINS TWO MONOMERS THAT ARE NOT RELATED TO THE BIOLOGICAL FORM. THE BIOLOGICAL UNIT IS A FIBER. IT IS UNKNOWN AT THE MOMENT HOW INDIVIDUAL SUBUNITS ARE ASSEMBLED IN VIVO.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Type II secretion protein / Type II secretion system / Type II secretion pathway related protein


Mass: 13733.197 Da / Num. of mol.: 2 / Fragment: UNP residues 24-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: 86-24 / Gene: ECO57PM05, etpG, GSPG, L7036 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BSV8

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.0M Na citrate, 0.1M CHES pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 30, 2008
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.78→35.01 Å / Num. all: 41532 / Num. obs: 39113 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.85 Å2 / Rmerge(I) obs: 0.064
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.78-1.820.5451.852892732188.8
1.82-1.870.4132.657452883194.5
1.87-1.930.3343.252422634193.5
1.93-1.990.2424.154562743195
1.99-2.050.2014.852062620194.3
2.05-2.130.1615.949222474194.9
2.13-2.210.1267.747712397194.8
2.21-2.30.1218.147382379194.8
2.3-2.40.0939.944342227194.5
2.4-2.510.08310.742052115194.9
2.51-2.650.07711.741942108195.4
2.65-2.810.06513.837991908196
2.81-3.010.04618.135821797194.4
3.01-3.250.03821.434001708195.1
3.25-3.560.032729731493194.4
3.56-3.980.02332.227531382194
3.98-4.590.02138.324971256193.5
4.59-5.620.02135.620231015194.2
5.62-7.950.0236.71601804194.1
7.95-35.010.01744.8869438194.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.17 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35 Å
Translation2.5 Å35 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FU1

3fu1


Resolution: 1.78→35.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.858 / SU B: 6.809 / SU ML: 0.097 / SU R Cruickshank DPI: 0.142 / SU Rfree: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 999 5 %RANDOM
Rwork0.168 ---
all0.17 20713 --
obs0.17 19947 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 39.04 Å2 / Biso mean: 12.079 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20.44 Å2-0.04 Å2
2--0.63 Å2-0.95 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.78→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 37 266 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221952
X-RAY DIFFRACTIONr_bond_other_d0.0010.021367
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9962665
X-RAY DIFFRACTIONr_angle_other_deg0.853.0043292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.725239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81524.951103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4631517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_mcbond_it0.4131.51184
X-RAY DIFFRACTIONr_mcbond_other0.111.5468
X-RAY DIFFRACTIONr_mcangle_it0.80221929
X-RAY DIFFRACTIONr_scbond_it1.5163768
X-RAY DIFFRACTIONr_scangle_it2.3624.5732
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 70 -
Rwork0.275 1356 -
all-1426 -
obs--92.84 %
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)
10.2461-1.1617-1.24425.54115.68067.21130.0415-0.03290.0194-0.24040.1594-0.0873-0.21720.3513-0.20090.0967-0.00690.00340.2267-0.06690.14085.1667.55515.941
22.9217-0.13070.07953.66570.5742.5214-0.0947-0.24890.14020.1190.03830.0393-0.0675-0.07920.05640.01120.0149-0.00210.0425-0.01110.0321-0.39623.81241.685
32.1175-1.05680.14472.5521.15881.56240.00880.1062-0.29350.05220.03530.06620.14210.0579-0.04410.037-0.00490.0120.03980.0010.07192.73811.84232.622
40.9017-0.89390.58526.77156.922210.01130.01870.04050.117-0.26050.3389-0.4771-0.27320.5906-0.35760.0848-0.00320.02320.12090.01740.1187-2.55216.765-19.993
53.629-0.75210.18291.69810.71171.6587-0.0894-0.5117-0.02580.17880.07520.00490-0.09740.01410.03770.00690.00460.0987-0.00180.0292-8.16427.6110.527
63.26050.43810.92041.75851.07312.7696-0.0131-0.0025-0.2083-0.0212-0.0145-0.03570.13690.00460.02750.03870.01710.02640.02930.00360.0337-0.3218.987-0.647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 42
2X-RAY DIFFRACTION2A43 - 81
3X-RAY DIFFRACTION3A82 - 131
4X-RAY DIFFRACTION4B18 - 35
5X-RAY DIFFRACTION5B36 - 90
6X-RAY DIFFRACTION6B91 - 136

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