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- PDB-4s36: Crystal structure of the C-terminal domain of R2 pyocin membrane-... -

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Basic information

Entry
Database: PDB / ID: 4s36
TitleCrystal structure of the C-terminal domain of R2 pyocin membrane-piercing spike
ComponentsPhage baseplate protein
KeywordsMETAL BINDING PROTEIN / Cell Puncturing Device / Trimer / beta-helix / Iron-binding / Outer cell membrane piercing
Function / homologyPhage baseplate assembly protein V/Gp45 / 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 / metal ion binding / : / Baseplate assembly protein V
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBrowning, C.B. / Leiman, P.G. / Shneider, M.M.
CitationJournal: To be Published
Title: Crystal structure of the C-terminal domain of R2 pyocin membrane-piercing spike
Authors: Browning, C.B. / Leiman, P.G. / Shneider, M.M.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Derived calculations
Revision 2.0Jul 12, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.ptnr1_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage baseplate protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4862
Polymers9,4301
Non-polymers561
Water2,126118
1
A: Phage baseplate protein
hetero molecules

A: Phage baseplate protein
hetero molecules

A: Phage baseplate protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4586
Polymers28,2913
Non-polymers1683
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14300 Å2
ΔGint-163 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.205, 46.205, 144.954
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-201-

FE

21A-304-

HOH

31A-331-

HOH

41A-333-

HOH

51A-356-

HOH

61A-366-

HOH

71A-367-

HOH

81A-391-

HOH

91A-413-

HOH

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Components

#1: Protein Phage baseplate protein / VR2 protein


Mass: 9430.291 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 96-185)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: VR2, gpV, D480_28305, JF43_02945, NCGM1900_0632, NCGM1984_0630
Plasmid: pEEVa2 (pET-23a derivate with a TEV cleavage site) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9S581
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 34% PEG 400, 200mM NaSO4, 100mM Na acetate, pH 5.0, 15mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→72.48 Å / Num. all: 16655 / Num. obs: 16695 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 27 % / Rmerge(I) obs: 0.036 / Rsym value: 0.037 / Net I/σ(I): 59.3
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2314 / Rsym value: 0.616 / % possible all: 97.3

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→40.015 Å / SU ML: 0.15 / σ(F): 1.53 / Phase error: 14.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 1509 5.07 %
Rwork0.1492 --
obs0.151 16615 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→40.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms665 0 1 118 784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008768
X-RAY DIFFRACTIONf_angle_d1.2741061
X-RAY DIFFRACTIONf_dihedral_angle_d9.958279
X-RAY DIFFRACTIONf_chiral_restr0.081123
X-RAY DIFFRACTIONf_plane_restr0.007140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50960.24321510.17982471X-RAY DIFFRACTION96
1.5096-1.56360.18111660.12482521X-RAY DIFFRACTION99
1.5636-1.62620.15371410.11252536X-RAY DIFFRACTION99
1.6262-1.70020.16471370.10372626X-RAY DIFFRACTION100
1.7002-1.78980.15161370.10142569X-RAY DIFFRACTION100
1.7898-1.9020.18651480.09492564X-RAY DIFFRACTION100
1.902-2.04880.13921190.08982598X-RAY DIFFRACTION100
2.0488-2.2550.13731460.10142590X-RAY DIFFRACTION100
2.255-2.58120.20061290.13312583X-RAY DIFFRACTION99
2.5812-3.25180.20971110.17652607X-RAY DIFFRACTION100
3.2518-40.02970.21451240.20482596X-RAY DIFFRACTION99

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