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- PDB-2jbg: crystal structure of the mutant N560A of the nuclease domain of C... -

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Basic information

Entry
Database: PDB / ID: 2jbg
Titlecrystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7
Components
  • COLICIN E7
  • COLICIN-E7 IMMUNITY PROTEIN
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / ZINC / TOXIN / PLASMID / NUCLEASE / HYDROLASE / ANTIBIOTIC / H-N-H MOTIF / BACTERIOCIN / ENDONUCLEASE / METAL-BINDING / ANTIMICROBIAL / DNA HYDROLYSIS / BACTERIOCIN IMMUNITY / HIS METAL FINGER MOTIF
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 (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuang, H. / Yuan, H.S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Conserved Asparagine in the Hnh Motif Serves an Important Structural Role in Metal Finger Endonucleases.
Authors: Huang, H. / Yuan, H.S.
History
DepositionDec 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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_database_status.status_code_sf / _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: COLICIN-E7 IMMUNITY PROTEIN
B: COLICIN E7
C: COLICIN-E7 IMMUNITY PROTEIN
D: COLICIN E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1758
Polymers49,8524
Non-polymers3234
Water5,693316
1
A: COLICIN-E7 IMMUNITY PROTEIN
B: COLICIN E7
C: COLICIN-E7 IMMUNITY PROTEIN
D: COLICIN E7
hetero molecules

A: COLICIN-E7 IMMUNITY PROTEIN
B: COLICIN E7
C: COLICIN-E7 IMMUNITY PROTEIN
D: COLICIN E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35016
Polymers99,7048
Non-polymers6468
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.180, 62.683, 74.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-2002-

HOH

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Components

#1: Protein COLICIN-E7 IMMUNITY PROTEIN / COLICIN E7 IMMUNITY PROTEIN / IMME7 / MICROCIN-E7 IMMUNITY PROTEIN


Mass: 9906.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Plasmid: PQE70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: Q03708, Hydrolases; Acting on ester bonds
#2: Protein COLICIN E7 / COLICIN-E7


Mass: 15019.079 Da / Num. of mol.: 2 / Fragment: NUCLEASE DOMAIN, RESIDUES 446-576 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Plasmid: PQE70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, ASN 560 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASN 560 TO ALA

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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: 56.1 %
Crystal growpH: 4.6
Details: 20 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE TRIHYDRATE AT PH 4.6

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 2, 2004 / Details: MIRRORS
RadiationMonochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→37.4 Å / Num. obs: 29109 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.07 / Net I/σ(I): 27.1
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.38 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MZ8

1mz8


Resolution: 2.2→37.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 286152.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2831 10 %RANDOM
Rwork0.202 ---
obs0.202 28439 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6275 Å2 / ksol: 0.372362 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20 Å20 Å2
2--1.02 Å20 Å2
3---3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 12 316 3678
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.492.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 447 10 %
Rwork0.219 4034 -
obs--94 %
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

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