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Basic information

Entry
Database: PDB / ID: 2zrr
TitleCrystal structure of an immunity protein that contributes to the self-protection of bacteriocin-producing Enterococcus mundtii 15-1A
ComponentsMundticin KS immunity protein
KeywordsANTIMICROBIAL PROTEIN / antiparallel four-helix bundle
Function / homologyde novo design (two linked rop proteins) - #140 / : / Lactococcin-A immunity protein-like / Bacteriocin immunity protein family / bacteriocin immunity / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / Bacteriocin immunity protein
Function and homology information
Biological speciesEnterococcus mundtii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsJeon, H.J. / Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure and mutagenic analysis of a bacteriocin immunity protein, Mun-im
Authors: Jeon, H.J. / Noda, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
History
DepositionAug 30, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Mundticin KS immunity protein


Theoretical massNumber of molelcules
Total (without water)13,2901
Polymers13,2901
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.710, 73.780, 94.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-240-

HOH

31A-263-

HOH

41A-281-

HOH

51A-284-

HOH

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Components

#1: Protein Mundticin KS immunity protein


Mass: 13290.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus mundtii (bacteria) / Strain: 15-1A / Gene: orf8 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B9A7V6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUNECE DATABSE OF THIS PROTEIN HAS BEEN DEPOSITED TO DDBJ. ACCESSION CODE AB454504. IT WILL ...THE SEQUNECE DATABSE OF THIS PROTEIN HAS BEEN DEPOSITED TO DDBJ. ACCESSION CODE AB454504. IT WILL BE OPENED WHEN THIS FILE IS PUBLISHED.

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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: 1.89 Å3/Da / Density % sol: 34.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 3.1M sodium formate, 0.1M sodium citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 9138 / Num. obs: 9138 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 39.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.8 / Num. unique all: 644 / Rsym value: 0.368 / % possible all: 69.4

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 450 5.6 %RANDOM
Rwork0.228 ---
obs0.228 8042 83.4 %-
all-8042 --
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms648 0 0 94 742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.651.5
X-RAY DIFFRACTIONx_mcangle_it4.292
X-RAY DIFFRACTIONx_scbond_it4.662
X-RAY DIFFRACTIONx_scangle_it7.062.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.076 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 25 7.2 %
Rwork0.33 323 -
obs-464 38.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.pro
X-RAY DIFFRACTION2toph19.sol

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