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- PDB-3gn9: Crystal structure of the major pseudopilin from the type 2 secret... -

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Basic information

Entry
Database: PDB / ID: 3gn9
TitleCrystal structure of the major pseudopilin from the type 2 secretion system of Vibrio vulnificus
ComponentsType II secretory pathway, pseudopilin EpsG
KeywordsPROTEIN TRANSPORT / GENERAL SECRETORY PATHWAY / MAJOR PILIN / COMPLEX / Methylation
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / 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
D-MALATE / Type II secretion system core protein G / Type II secretion system core protein G
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 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
DepositionMar 16, 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 / 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 / _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 secretory pathway, pseudopilin EpsG
B: Type II secretory pathway, pseudopilin EpsG
C: Type II secretory pathway, pseudopilin EpsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1468
Polymers37,7573
Non-polymers3885
Water4,792266
1
A: Type II secretory pathway, pseudopilin EpsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7603
Polymers12,5861
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type II secretory pathway, pseudopilin EpsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6262
Polymers12,5861
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Type II secretory pathway, pseudopilin EpsG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7603
Polymers12,5861
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.180, 104.510, 55.410
Angle α, β, γ (deg.)90.000, 106.160, 90.000
Int Tables number5
Space group name H-MC121
DetailsTHIS CRYSTAL FORM CONTAINS THREE 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

#1: Protein Type II secretory pathway, pseudopilin EpsG


Mass: 12585.797 Da / Num. of mol.: 3 / Fragment: UNP residues 26-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: MO6-24 / Gene: EPSG, VV1_0874 / Plasmid: pCDF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DDT3, UniProt: A0A3Q0L2Q1*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: 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: 3.69 Å3/Da / Density % sol: 66.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.95M DL-Malic acid pH 5.0, 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: 1.5418 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→38.9 Å / Num. all: 90808 / Num. obs: 78730 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 38.722 Å2 / Rmerge(I) obs: 0.029
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.86-1.910.4861.7119255544181.5
1.91-1.960.3142.6116375365182.1
1.96-2.020.2423.3113925260183.3
2.02-2.080.1814.3111335154183.3
2.08-2.150.1415.4109235083184.6
2.15-2.220.116.7105834956185.4
2.22-2.310.0957.9100794738184.9
2.31-2.40.06810.299204679186.5
2.4-2.510.0541394484475186.9
2.51-2.630.0441591054336188.2
2.63-2.770.03718.486854159188.6
2.77-2.940.0323.282143971189.1
2.94-3.140.02328.576833729189.9
3.14-3.40.0231.571193478190.7
3.4-3.720.01936.766093266190.3
3.72-4.160.01840.559242951192.1
4.16-4.80.01741.653592686193
4.8-5.880.01641.244732259194.4
5.88-8.320.0174234461748194.3
8.32-38.90.01643.11699893187.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.73 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.47 Å
Translation2.5 Å35.47 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 1FU1

1fu1


Resolution: 1.86→38.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.821 / SU B: 7.356 / SU ML: 0.096 / SU R Cruickshank DPI: 0.105 / SU Rfree: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102 / 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
Rfree0.204 2272 5.1 %RANDOM
Rwork0.178 ---
all0.179 45957 --
obs0.179 44693 97.25 %-
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: 71.27 Å2 / Biso mean: 34.969 Å2 / Biso min: 13.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å22.55 Å2
2---3.27 Å20 Å2
3---4.79 Å2
Refinement stepCycle: LAST / Resolution: 1.86→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 21 266 2884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222722
X-RAY DIFFRACTIONr_bond_other_d0.0010.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9743700
X-RAY DIFFRACTIONr_angle_other_deg0.84534502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70426.62142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91115456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.258159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
X-RAY DIFFRACTIONr_mcbond_it0.5711.51685
X-RAY DIFFRACTIONr_mcbond_other0.1511.5693
X-RAY DIFFRACTIONr_mcangle_it1.03922698
X-RAY DIFFRACTIONr_scbond_it1.74931037
X-RAY DIFFRACTIONr_scangle_it2.7394.5993
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 173 -
Rwork0.305 3090 -
all-3263 -
obs--95.44 %
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)
16.50323.76351.22865.89150.49821.5945-0.01850.07090.2121-0.15960.02890.56040.2648-0.2334-0.01050.134-0.0509-0.02670.07220.00570.0591-17.524-8.618-4.399
25.11123.64952.05936.73141.95624.0987-0.18770.40690.1296-0.69940.12810.5420.3564-0.4020.05950.1977-0.0862-0.05670.1484-0.0050.0608-21.091-12.94-11.244
36.7081-3.40140.24793.67570.22061.52730.03920.1230.3996-0.1198-0.2103-0.0095-0.2793-0.27550.1710.09110.0589-0.05110.0584-0.03480.2106-18.2617.968-2.929
49.5988-3.3725-0.00494.46760.71741.7650.06840.2626-0.372-0.2159-0.20020.7985-0.1278-0.48760.13170.15770.0884-0.05840.1663-0.03820.3187-27.05817.466-2.779
51.6571-0.73960.35923.2774-1.85726.21490.13250.58580.4469-0.6909-0.036-0.07450.1486-0.2889-0.09660.22710.04320.03440.26530.1920.1414-4.5947.675-23.415
616.4988.963-5.476912.5642-8.184212.559-0.01660.3662-0.1096-1.2180.46120.48880.0931-2.1731-0.44460.76680.3202-0.19831.00570.27470.345-15.59113.534-33.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 78
2X-RAY DIFFRACTION2A79 - 137
3X-RAY DIFFRACTION3B27 - 78
4X-RAY DIFFRACTION4B79 - 137
5X-RAY DIFFRACTION5C27 - 115
6X-RAY DIFFRACTION6C116 - 137

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