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- PDB-7cei: THE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITS INHIBIT... -

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Basic information

Entry
Database: PDB / ID: 7cei
TitleTHE ENDONUCLEASE DOMAIN OF COLICIN E7 IN COMPLEX WITH ITS INHIBITOR IM7 PROTEIN
Components(PROTEIN (COLICIN E7 IMMUNITY PROTEIN)) x 2
KeywordsIMMUNE SYSTEM / DNASE / E-GROUP COLICINS / PROTEIN-PROTEIN INTERACTION / PROTEIN RECOGNITION
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 / 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, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / 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, DNase domain superfamily / Colicin/Pyocin-S2, DNase domain / 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 / HNH nucleases / HNH nuclease / 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
Colicin-E7 immunity protein / Colicin-E7
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKo, T.P. / Liao, C.C. / Ku, W.Y. / Chak, K.F. / Yuan, H.S.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.
Authors: Ko, T.P. / Liao, C.C. / Ku, W.Y. / Chak, K.F. / Yuan, H.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: The Crystal Structure of the Immunity Protein of Colicin E7 Suggests a Possible Colicin-Interacting Surface.
Authors: Chak, K.-F. / Safo, M.K. / Ku, W.-Y. / Hsieh, S.-Y. / Yuan, H.S.
History
DepositionSep 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _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: PROTEIN (COLICIN E7 IMMUNITY PROTEIN)
B: PROTEIN (COLICIN E7 IMMUNITY PROTEIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4383
Polymers33,3732
Non-polymers651
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.440, 76.020, 119.990
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-701-

HOH

21A-702-

HOH

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Components

#1: Protein PROTEIN (COLICIN E7 IMMUNITY PROTEIN) / IM7


Mass: 9906.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: CEIE7 / Gene (production host): CEIE7 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q03708
#2: Protein PROTEIN (COLICIN E7 IMMUNITY PROTEIN) / COLE7 DNASE DOMAIN


Mass: 23465.652 Da / Num. of mol.: 1 / Fragment: ENDONUCLEASE DOMAIN / Source method: isolated from a natural source
Source: (natural) Escherichia coli str. K12 substr. (bacteria)
Plasmid: PCOLE7 / Species: Escherichia coli / Strain: W3110 / References: UniProt: Q47112
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.8 Å3/Da / Density % sol: 54 %
Crystal growpH: 6
Details: 15 MG/ML PROTEIN COMPLEX, 5 MM NA CITRATE, 0.25 M NH4 ACETATE, 10% PEG4000, PH 6.0 VAPOR DIFFUSION AGAINST 22.5% PEG4000
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
25 mMsodium citrate1drop
30.25 Mammonium acetate1drop
410 %PEG40001drop
522.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 12090 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 2 / Rsym value: 0.191 / % possible all: 76.3
Reflection
*PLUS
Num. measured all: 38306

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CEI

1cei


Resolution: 2.3→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 842 8 %RANDOM
Rwork0.203 ---
obs0.203 10498 76.8 %-
Displacement parametersBiso mean: 37.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-40 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 1 162 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.012
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.05
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.546
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.1081.5
X-RAY DIFFRACTIONx_mcangle_it1.9852
X-RAY DIFFRACTIONx_scbond_it1.3622
X-RAY DIFFRACTIONx_scangle_it2.2192.5
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.314 32 8 %
Rwork0.305 351 -
obs--43.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.05
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.546
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.314 / % reflection Rfree: 8 % / Rfactor Rwork: 0.305

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