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- PDB-2bl8: 1.6 Angstrom crystal structure of EntA-im: a bacterial immunity p... -

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Basic information

Entry
Database: PDB / ID: 2bl8
Title1.6 Angstrom crystal structure of EntA-im: a bacterial immunity protein conferring immunity to the antimicrobial activity of the pediocin-like bacteriocin, enterocin A
ComponentsENTEROCINE A IMMUNITY PROTEIN
KeywordsBACTERIAL PROTEIN / ENTEROCIN A / ORF2 PROTEIN / IMMUNITY
Function / homology
Function and homology information


bacteriocin immunity
Similarity search - Function
Ta0600-like / Ta0600-like superfamily / Lactococcin-A immunity protein-like / Bacteriocin immunity protein family / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Bacteriocin immunity protein
Similarity search - Component
Biological speciesENTEROCOCCUS FAECIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJohnsen, L. / Dalhus, B. / Leiros, I. / Nissen-Meyer, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: 1.6-A Crystal Structure of Enta-Im: A Bacterial Immunity Protein Conferring Immunity to the Antimicrobial Activity of the Pediocin-Like Bacteriocin Enterocin A
Authors: Johnsen, L. / Dalhus, B. / Leiros, I. / Nissen-Meyer, J.
History
DepositionMar 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENTEROCINE A IMMUNITY PROTEIN
B: ENTEROCINE A IMMUNITY PROTEIN
C: ENTEROCINE A IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0805
Polymers36,7023
Non-polymers3782
Water6,485360
1
A: ENTEROCINE A IMMUNITY PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2341
Polymers12,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENTEROCINE A IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6123
Polymers12,2341
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ENTEROCINE A IMMUNITY PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,2341
Polymers12,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.330, 42.370, 66.240
Angle α, β, γ (deg.)90.00, 111.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2036-

HOH

21C-2071-

HOH

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Components

#1: Protein ENTEROCINE A IMMUNITY PROTEIN


Mass: 12233.946 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECIUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q47785
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.3 Å3/Da / Density % sol: 45.6 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8727
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8727 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 38124 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.4 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEITdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BL7

2bl7


Resolution: 1.6→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1165 2.9 %RANDOM
Rwork0.2192 ---
obs0.2192 38124 95.3 %-
Solvent computationBsol: 54.1432 Å2 / ksol: 0.368412 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.103 Å20 Å2-3.448 Å2
2--1.788 Å20 Å2
3----1.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 26 360 2618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004735
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.18183
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.66 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.374 119 3.4 %
Rwork0.302 3492 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5FLC.PARAMFLC.TOP

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