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- PDB-4fzm: Crystal structure of the bacteriocin syringacin M from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 4fzm
TitleCrystal structure of the bacteriocin syringacin M from Pseudomonas syringae pv. tomato DC3000
ComponentsBacteriocin
KeywordsANTIMICROBIAL PROTEIN / Phosphatase / Divalent cation 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 - #880 / 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 / MAD / Resolution: 2.83 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_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.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_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_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

Downloads & links

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Assembly

Deposited unit
A: Bacteriocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8163
Polymers30,7141
Non-polymers1022
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bacteriocin
hetero molecules

A: Bacteriocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6336
Polymers61,4292
Non-polymers2044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/21
Buried area1810 Å2
ΔGint-35 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.687, 159.687, 100.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Bacteriocin /


Mass: 30714.273 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 7% w/v PEG 8000, 30% v/v ethylene glycol 0.03 M CaCl2, 0.03 M MgCl2, 5% dimethyl sulfoxide, 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: I04 / Wavelength: 0.9795, 0.9796, 0.9253
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.92531
ReflectionResolution: 2.83→46.34 Å / Num. all: 17330 / Num. obs: 17330 / % possible obs: 99.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 102.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.5
Reflection shellResolution: 2.83→2.91 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1337 / % possible all: 100

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Processing

Software
NameVersionClassification
EDNAdata collection
SHARPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.83→46.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 19.822 / SU ML: 0.174 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23914 929 5.1 %RANDOM
Rwork0.2004 ---
all0.20227 17330 --
obs0.20227 17330 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.83→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 5 35 2123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022152
X-RAY DIFFRACTIONr_bond_other_d0.0010.021423
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9562937
X-RAY DIFFRACTIONr_angle_other_deg1.09633473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6735279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.49724.53697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88715320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.321513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
LS refinement shellResolution: 2.835→2.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 63 -
Rwork0.353 1125 -
obs--99.75 %
Refinement TLS params.Method: refined / Origin x: -70.0341 Å / Origin y: 16.354 Å / Origin z: -10.0954 Å
111213212223313233
T0.6911 Å20.0556 Å2-0.0155 Å2-0.3659 Å20.1345 Å2--0.4552 Å2
L7.8304 °22.9152 °2-2.3017 °2-4.1527 °2-2.135 °2--4.2854 °2
S0.1313 Å °-1.4122 Å °-0.7912 Å °0.5507 Å °-0.0534 Å °-0.3122 Å °-0.3917 Å °0.3978 Å °-0.0778 Å °

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