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- PDB-4uhv: The structure of VgrG1, the needle tip of the bacterial Type VI S... -

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Basic information

Entry
Database: PDB / ID: 4uhv
TitleThe structure of VgrG1, the needle tip of the bacterial Type VI Secretion System
ComponentsVGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
KeywordsSTRUCTURAL PROTEIN / VGRG1 / VIRULENCE / TOXIN / EFFECTOR / PUNCTURING DEVICE / SPIKE / T6SS / P. AERUGINOSA
Function / homology
Function and homology information


type VI protein secretion system complex / protein secretion by the type VI secretion system / extracellular region
Similarity search - Function
Light-harvesting Protein - #110 / Pnp Oxidase; Chain A - #50 / Gp5 N-terminal domain / Baseplate protein-like domains / Light-harvesting Protein / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail protein beta-alpha-beta fold / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) ...Light-harvesting Protein - #110 / Pnp Oxidase; Chain A - #50 / Gp5 N-terminal domain / Baseplate protein-like domains / Light-harvesting Protein / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Phage tail protein beta-alpha-beta fold / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / : / Pnp Oxidase; Chain A / 3-Layer(bab) Sandwich / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Type VI secretion system spike protein VgrG1a
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSpinola-Amilibia, M. / Davo-Siguero, I. / Ruiz, F.M. / Santillana, E. / Medrano, F.J. / Romero, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: The Structure of Vgrg1 from Pseudomonas Aeruginosa, the Needle Tip of the Bacterial Type Vi Secretion System
Authors: Spinola-Amilibia, M. / Davo-Siguero, I. / Ruiz, F.M. / Santillana, E. / Medrano, F.J. / Romero, A.
History
DepositionMar 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
B: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,82953
Polymers147,1832
Non-polymers1,64651
Water11,602644
1
B: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules

B: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules

B: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,91799
Polymers220,7753
Non-polymers3,14296
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area53100 Å2
ΔGint-295.3 kcal/mol
Surface area102870 Å2
MethodPQS
2
A: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules

A: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules

A: VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,57160
Polymers220,7753
Non-polymers1,79657
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area52980 Å2
ΔGint-282.6 kcal/mol
Surface area105410 Å2
MethodPQS
Unit cell
Length a, b, c (Å)78.620, 78.620, 430.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein VGRG1, VALINE-GLYCINE REPEAT PROTEIN G1


Mass: 73591.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET29_VGRG1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: Q9I741
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.62 Å3/Da / Density % sol: 53.1 % / Description: TWINNED DATA, L-TEST OF 0.34
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1 M HEPES PH 7.2, 0.2 M LITHIUM SULPHATE AND 38 % MPD; THEN THE CRYSTAL WAS SOAKED IN 2 MM NEODYMIUM (III) SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.72785
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2014 / Details: KB MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72785 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11K, H, -L20.5
ReflectionResolution: 1.88→86.06 Å / Num. obs: 111022 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 6
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.1 / % possible all: 56.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MTK

4mtk


Resolution: 2→71.73 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.893 / SU B: 3.812 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24845 4702 5 %RANDOM
Rwork0.22332 ---
obs0.22457 90119 93.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.78 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å20 Å20 Å2
2--5.92 Å20 Å2
3----11.84 Å2
Refinement stepCycle: LAST / Resolution: 2→71.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10189 0 51 644 10884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910462
X-RAY DIFFRACTIONr_bond_other_d0.0020.029696
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.95114185
X-RAY DIFFRACTIONr_angle_other_deg0.934322228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.67351299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69223.43554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.317151641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.13115105
X-RAY DIFFRACTIONr_chiral_restr0.0980.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022619
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_it1.8523.7355166
X-RAY DIFFRACTIONr_mcbond_other1.8513.7355165
X-RAY DIFFRACTIONr_mcangle_it2.7715.5996457
X-RAY DIFFRACTIONr_mcangle_other2.7715.5996458
X-RAY DIFFRACTIONr_scbond_it1.5263.7615296
X-RAY DIFFRACTIONr_scbond_other1.5243.765294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2085.6337722
X-RAY DIFFRACTIONr_long_range_B_refined5.23229.99111876
X-RAY DIFFRACTIONr_long_range_B_other5.12729.98611798
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 313 -
Rwork0.249 6063 -
obs--85.86 %

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