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- PDB-1bxi: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1bxi
TitleCRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9
Components
  • PROTEIN (COLICIN E9 IMMUNITY PROTEIN)
  • PROTEIN (COLICIN E9)
KeywordsIMMUNE SYSTEM / COLICINS / ENDONUCLEASE / PROTEIN-PROTEIN INTERACTION
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / : / toxic substance binding / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / protein domain specific binding / protein-containing complex / metal ion binding
Similarity search - Function
Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / His-Me finger superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Colicin-E9 / Colicin-E9 immunity protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsKuhlmann, U.C. / Kleanthous, C. / James, R. / Moore, G.R. / Hemmings, A.M.
Citation
Journal: Thesis / Year: 1998
Title: Crystal Structure of the E.Coli Colicin E9 DNase Domain With its Cognate Immunity Protein Im9
Authors: Kuhlmann, U.C.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Structural and Mechanistic Basis of Immunity Toward Endonuclease Colicins
Authors: Kleanthous, C. / Kuhlmann, U.C. / Pommer, A.J. / Radford, N.Ferguson S.E. / Moore, G.R. / James, R. / Hemmings, A.M.
History
DepositionOct 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (COLICIN E9 IMMUNITY PROTEIN)
B: PROTEIN (COLICIN E9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8924
Polymers24,7382
Non-polymers1542
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-23 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.850, 51.960, 87.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (COLICIN E9 IMMUNITY PROTEIN)


Mass: 9524.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: E9IMM / Plasmid: PRJ345 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P13479
#2: Protein PROTEIN (COLICIN E9)


Mass: 15213.811 Da / Num. of mol.: 1 / Fragment: DNASE DOMAIN, RESIDUES 450-581
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: COLE9 / Plasmid: PRJ353 / Gene (production host): COLE9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): B834 (DE3) / References: UniProt: P09883
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growpH: 5.3 / Details: 24%(W/V)PEG 4K, 0.1MM SODIUM-ACETATE, PH5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.979,0.9795,0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97951
30.91
ReflectionResolution: 2.05→20 Å / Num. obs: 13096 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.061 / Net I/σ(I): 22.8
Reflection shellResolution: 2.05→2.15 Å / Mean I/σ(I) obs: 6.7 / % possible all: 99.9

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→8 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.315 620 5 %RANDOM
Rwork0.218 ---
obs-12529 100 %-
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 6 103 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0460.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7412
X-RAY DIFFRACTIONp_mcangle_it4.0373
X-RAY DIFFRACTIONp_scbond_it2.8552
X-RAY DIFFRACTIONp_scangle_it4.273
X-RAY DIFFRACTIONp_plane_restr0.0194
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2730.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2190.3
X-RAY DIFFRACTIONp_planar_tor6.77
X-RAY DIFFRACTIONp_staggered_tor24.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor15

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