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- PDB-4qko: The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity ... -

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Basic information

Entry
Database: PDB / ID: 4qko
TitleThe Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms
Components
  • Pyocin-S2
  • Pyocin-S2 immunity protein
KeywordsANTIMICROBIAL PROTEIN / HNH Nuclease Domain / Colicin Nuclease Immunity Protein Complex / Bacteriocin / Bacterial Cytotoxin
Function / homology
Function and homology information


cytolysis / bacteriocin immunity / toxic substance binding / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / signaling receptor binding / metal ion binding
Similarity search - Function
Pyocin S killer protein / S-type Pyocin / Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain ...Pyocin S killer protein / S-type Pyocin / Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/pyocin, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / HNH nucleases / His-Me finger superfamily / HNH nuclease / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Pyocin-S2 immunity protein / Pyocin-S2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGrinter, R. / Josts, I. / Roszak, A.W. / Cogdell, C.J. / Walker, D.
CitationJournal: To be Published
Title: Structural Insights into pyocin S2
Authors: Grinter, R. / Josts, I. / McCaughey, L.C. / Roszak, A.W. / Walen, K.I. / Kelly, S. / Byron, O. / Walker, D.
History
DepositionJun 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Pyocin-S2 immunity protein
B: Pyocin-S2
C: Pyocin-S2 immunity protein
D: Pyocin-S2
E: Pyocin-S2 immunity protein
F: Pyocin-S2
G: Pyocin-S2 immunity protein
H: Pyocin-S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,47347
Polymers102,5808
Non-polymers2,89439
Water14,682815
1
A: Pyocin-S2 immunity protein
B: Pyocin-S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1499
Polymers25,6452
Non-polymers5047
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-12 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: Pyocin-S2 immunity protein
D: Pyocin-S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,46813
Polymers25,6452
Non-polymers82311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-16 kcal/mol
Surface area11090 Å2
MethodPISA
3
E: Pyocin-S2 immunity protein
F: Pyocin-S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,46813
Polymers25,6452
Non-polymers82311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-14 kcal/mol
Surface area11070 Å2
MethodPISA
4
G: Pyocin-S2 immunity protein
H: Pyocin-S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38812
Polymers25,6452
Non-polymers74310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-14 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.390, 114.420, 120.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pyocin-S2 immunity protein


Mass: 11127.503 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: imm2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q06579
#2: Protein
Pyocin-S2 / Killer protein


Mass: 14517.398 Da / Num. of mol.: 4
Fragment: Nuclease Domain, C-terminal fragement residues 556-689
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: pys2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q06584, Hydrolases; Acting on ester bonds
#3: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 815 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium Bromide, 20% PEG 3350, 0.1M Bis-Tris propane, 0.1% chymotrypsin, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2013
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→82.88 Å / Num. all: 83310 / Num. obs: 83310 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4379 / % possible all: 96.4

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U43

3u43


Resolution: 1.8→82.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.209 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(I): 2.3 / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21514 4150 5 %RANDOM
Rwork0.17155 ---
all0.17372 83310 --
obs0.17372 79092 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å20 Å2
2---1.08 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→82.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 39 815 7710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197155
X-RAY DIFFRACTIONr_bond_other_d0.0010.026830
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9519657
X-RAY DIFFRACTIONr_angle_other_deg0.869315809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18324.064342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.688151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3151550
X-RAY DIFFRACTIONr_chiral_restr0.1070.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218198
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021654
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_it1.99123544
X-RAY DIFFRACTIONr_mcbond_other1.98923543
X-RAY DIFFRACTIONr_mcangle_it2.9672.9754436
X-RAY DIFFRACTIONr_mcangle_other2.9672.9764437
X-RAY DIFFRACTIONr_scbond_it2.9632.3953611
X-RAY DIFFRACTIONr_scbond_other2.9632.3963612
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6663.4035217
X-RAY DIFFRACTIONr_long_range_B_refined7.68217.7199121
X-RAY DIFFRACTIONr_long_range_B_other7.45216.9688779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 304 -
Rwork0.239 5628 -
obs--96.13 %
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)
10.1069-0.36090.03292.1807-0.30020.1671-0.0734-0.0073-0.02440.14590.09220.0088-0.0436-0.0329-0.01890.06390.00830.02530.01810.00290.059716.1476117.006826.7827
20.22760.0772-0.09030.94380.10410.06230.01870.00150.00590.0003-0.0057-0.0157-0.01160.0088-0.0130.03930.0048-0.0110.0232-0.00040.0558-3.840992.8660.2323
30.0132-0.10580.04691.724-0.11890.389-0.0099-0.0015-0.02260.11580.04290.1402-0.07940.0182-0.0330.04980.00560.03550.00430.0120.075931.6242131.0213-1.9459
40.30270.0125-0.19152.61140.34880.1897-0.01410.0020.107-0.10170.09720.08250.02030.0248-0.08310.04750.0172-0.03080.0155-0.00350.0735-17.3162112.485931.7042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 87
2X-RAY DIFFRACTION1B556 - 686
3X-RAY DIFFRACTION2C2 - 87
4X-RAY DIFFRACTION2D556 - 686
5X-RAY DIFFRACTION3E2 - 87
6X-RAY DIFFRACTION3F556 - 686
7X-RAY DIFFRACTION4G2 - 87
8X-RAY DIFFRACTION4H556 - 686

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