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- PDB-4fzn: Crystal structure of syringacin M mutant D232A from Pseudomonas s... -

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Basic information

Entry
Database: PDB / ID: 4fzn
TitleCrystal structure of syringacin M mutant D232A from Pseudomonas syringae pv. tomato DC3000
ComponentsBacteriocin
KeywordsANTIMICROBIAL PROTEIN / Phosphatase
Function / homology
Function and homology information


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 / MOLECULAR REPLACEMENT / Resolution: 3.12 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 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin


Theoretical massNumber of molelcules
Total (without water)30,5391
Polymers30,5391
Non-polymers00
Water48627
1


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

A: Bacteriocin


Theoretical massNumber of molelcules
Total (without water)61,0782
Polymers61,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/21
Buried area1240 Å2
ΔGint-14 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.350, 160.350, 100.740
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: 30539.068 Da / Num. of mol.: 1 / Mutation: D232A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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 % sol: 79.91 %
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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2011 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.12→40.09 Å / Num. all: 13347 / Num. obs: 13347 / % possible obs: 99.53 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 107.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.9
Reflection shellResolution: 3.12→3.2 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1018 / % possible all: 100

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FZM

4fzm


Resolution: 3.12→40.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 26.446 / SU ML: 0.209 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22359 697 5 %RANDOM
Rwork0.18211 ---
all0.18417 13347 --
obs0.18417 13347 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 3.12→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 0 27 2107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022146
X-RAY DIFFRACTIONr_bond_other_d0.0010.021416
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9552931
X-RAY DIFFRACTIONr_angle_other_deg0.93833457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.924.47996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99415319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7751513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
LS refinement shellResolution: 3.121→3.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 48 -
Rwork0.267 847 -
obs-847 99.89 %
Refinement TLS params.Method: refined / Origin x: -70.2903 Å / Origin y: 16.4942 Å / Origin z: -10.244 Å
111213212223313233
T0.838 Å20.0639 Å2-0.0516 Å2-0.3674 Å20.1869 Å2--0.4807 Å2
L8.8857 °23.2724 °2-2.7261 °2-4.4333 °2-1.8499 °2--4.4816 °2
S0.1879 Å °-1.5592 Å °-0.8956 Å °0.6333 Å °-0.104 Å °-0.3555 Å °-0.4893 Å °0.429 Å °-0.0839 Å °

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