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- PDB-3fu1: Crystal structure of the major pseudopilin from the type 2 secret... -

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Basic information

Entry
Database: PDB / ID: 3fu1
TitleCrystal structure of the major pseudopilin from the type 2 secretion system of Vibrio cholerae
ComponentsGeneral secretion pathway protein G
KeywordsPROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / MAJOR PILIN / COMPLEX / Methylation / Transport
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
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 / Pilin-like ...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 / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type II secretion system core protein G
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 13, 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_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
A: General secretion pathway protein G
B: General secretion pathway protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4367
Polymers25,1592
Non-polymers2765
Water4,035224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-86 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.638, 64.749, 65.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS CRYSTAL FORM CONTAINS A DIMER, THAT IS NOT RELATED TO THE BIOLOGICAL FORM. BIOLOGICAL UNIT IS A FIBER, IT IS UNKNOWN AT THE MOMENT HOW INDIVIDUAL SUBUNITS ARE ASSEMBLED IN VIVO.

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Components

#1: Protein General secretion pathway protein G / Cholera toxin secretion protein epsG


Mass: 12579.704 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-146
Source method: isolated from a genetically manipulated source
Details: RESIDUES 26-137 / Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 569B / Gene: epsG, VC_2730 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45773
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 22.5% PEG 3350, 0.1M NA ACETATE, 0.04M ZN ACETATE, pH 5.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97946
SYNCHROTRONSSRL BL9-221.28344
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDNov 15, 2007
MARMOSAIC 325 mm CCD2CCDNov 15, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL SI(111)SINGLE WAVELENGTHMx-ray1
2DOUBLE CRYSTAL SI(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
21.283441
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 24.02 / Number: 113449 / Rmerge(I) obs: 0.087 / Χ2: 1.43 / D res high: 1.9 Å / D res low: 29 Å / Num. obs: 17045 / % possible obs: 97.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.092999.910.041.8966.8
3.254.0910010.0481.6737.2
2.843.2510010.0871.5937.3
2.582.8410010.1321.3317.3
2.392.5810010.1741.2717.3
2.252.3910010.2291.2817.3
2.142.2599.710.2911.2897
2.052.1498.110.3711.2456.3
1.972.0593.510.4781.2325.3
1.91.9778.810.5121.2264.1
ReflectionResolution: 1.9→29 Å / Num. obs: 17045 / % possible obs: 97.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.428 / Net I/σ(I): 24.016
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1373 / Χ2: 1.226 / % possible all: 78.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.04 Å
Translation2.5 Å29.04 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.875 / SU B: 6.78 / SU ML: 0.101 / SU R Cruickshank DPI: 0.172 / SU Rfree: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 830 4.9 %RANDOM
Rwork0.178 ---
obs0.18 16995 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.4 Å2 / Biso mean: 20.242 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 5 224 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221811
X-RAY DIFFRACTIONr_bond_other_d0.0010.021206
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9672464
X-RAY DIFFRACTIONr_angle_other_deg0.82632966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36626.70197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39515294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.411156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
X-RAY DIFFRACTIONr_mcbond_it0.4441.51129
X-RAY DIFFRACTIONr_mcbond_other0.1151.5470
X-RAY DIFFRACTIONr_mcangle_it0.83521808
X-RAY DIFFRACTIONr_scbond_it1.4293682
X-RAY DIFFRACTIONr_scangle_it2.3324.5653
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 53 -
Rwork0.268 916 -
all-969 -
obs--75.41 %
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)
13.7973-0.0326-0.03570.93940.20571.34760.03710.353-0.0364-0.0773-0.005-0.0212-0.0426-0.0362-0.03210.0390.00910.00190.0638-0.01450.0232-2.70114.294-9.76
25.44170.0603-0.72231.9252-0.03842.3798-0.19590.0022-0.88520.09690.0282-0.01340.4188-0.1250.16770.1799-0.03940.06580.0147-0.01830.2196-13.299-3.986-0.731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 137
2X-RAY DIFFRACTION2B26 - 137

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