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- PDB-4fzl: High resolution structure of truncated bacteriocin syringacin M f... -

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Basic information

Entry
Database: PDB / ID: 4fzl
TitleHigh resolution structure of truncated bacteriocin syringacin M from Pseudomonas syringae pv. tomato DC3000
ComponentsBacteriocin
KeywordsANTIMICROBIAL PROTEIN / Phosphatase / Calcium binding / Lipid II binding
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / metal ion binding
Similarity search - Function
DNA polymerase; domain 1 - #790 / Colicin M, catalytic domain / Colicin M / Colicin M / Beta-Lactamase / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bacteriocin, putative
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRoszak, A.W. / Grinter, R. / Cogdell, J.R. / Walker, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Crystal Structure of the Lipid II-degrading Bacteriocin Syringacin M Suggests Unexpected Evolutionary Relationships between Colicin M-like Bacteriocins.
Authors: Grinter, R. / Roszak, A.W. / Cogdell, R.J. / Milner, J.J. / Walker, D.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Feb 28, 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_asym_id / _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_asym_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_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.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: Bacteriocin
B: Bacteriocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,44620
Polymers53,4642
Non-polymers98218
Water9,926551
1
A: Bacteriocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,24210
Polymers26,7321
Non-polymers5109
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacteriocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,20410
Polymers26,7321
Non-polymers4729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bacteriocin
hetero molecules

A: Bacteriocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,44620
Polymers53,4642
Non-polymers98218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3360 Å2
ΔGint-44 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.810, 96.090, 64.270
Angle α, β, γ (deg.)90.00, 114.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bacteriocin /


Mass: 26731.904 Da / Num. of mol.: 2 / Fragment: UNP residues 38-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: PSPTO_0572 / Plasmid: pETMDC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q88A25

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Non-polymers , 5 types, 569 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 551 / 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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 8% w/v PEG 8000, 30% v/v ethylene glycol, 0.13 M CaCl2, 0.03 M MgCl2, 0.1 M Bicine/Tris base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2012 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 1.46→50.92 Å / Num. all: 106648 / Num. obs: 106648 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.6
Reflection shellResolution: 1.46→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2.9 / Num. unique all: 7853 / % possible all: 99.7

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→50.92 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.133 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20117 5244 5 %RANDOM
Rwork0.15157 ---
all0.15406 99482 --
obs0.15406 99482 97.88 %-
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 mean: 28.937 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å21.9 Å2
2---1.85 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.46→50.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 57 551 4253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193945
X-RAY DIFFRACTIONr_bond_other_d0.0010.022621
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.9495380
X-RAY DIFFRACTIONr_angle_other_deg1.1636410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7245523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58724.469179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79215609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9451524
X-RAY DIFFRACTIONr_chiral_restr0.1320.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02793
X-RAY DIFFRACTIONr_rigid_bond_restr6.87336566
X-RAY DIFFRACTIONr_sphericity_free40.4035198
X-RAY DIFFRACTIONr_sphericity_bonded24.14456835
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 382 -
Rwork0.307 7091 -
obs--96.28 %

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