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- PDB-2ivh: Crystal structure of the nuclease domain of ColE7 (H545Q mutant) ... -

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Basic information

Entry
Database: PDB / ID: 2ivh
TitleCrystal structure of the nuclease domain of ColE7 (H545Q mutant) in complex with an 18-bp duplex DNA
Components
  • 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3'
  • COLCIN-E7
KeywordsHYDROLASE / BACTERIOCIN / ENDONUCLEASE / ANTIMICROBIAL / METAL-BINDING / HYDROLASE-DNA COMPLEX / ZINC / PLASMID / NUCLEASE / ANTIBIOTIC
Function / homology
Function and homology information


extrachromosomal circular DNA / 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/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 ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / 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 / HNH nucleases / His-Me finger superfamily / HNH nuclease / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Colicin-E7
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, Y.T. / Yang, W.J. / Li, C.L. / Doudeva, L.G. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases.
Authors: Wang, Y.T. / Yang, W.J. / Li, C.L. / Doudeva, L.G. / Yuan, H.S.
History
DepositionJun 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
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
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_asym_id / _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_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLCIN-E7
B: 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3'
C: 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7484
Polymers25,6833
Non-polymers651
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.800, 106.800, 60.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein COLCIN-E7


Mass: 14651.606 Da / Num. of mol.: 1 / Fragment: NUCLEASE DOMAIN, RESIDUES 449-576 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#2: DNA chain 5'-D(*GP*GP*AP*AP*TP*TP*CP*GP*AP*TP *CP*GP*AP*AP*TP*TP*CP*C)-3'


Mass: 5515.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#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 / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PLASMID-CODED BACTERICIDAL PROTEIN IS AN ENDONUCLEASE ACTIVE ON BOTH SINGLE- AND DOUBLE- ...THIS PLASMID-CODED BACTERICIDAL PROTEIN IS AN ENDONUCLEASE ACTIVE ON BOTH SINGLE- AND DOUBLE-STRANDED DNA BUT WITH UNDEFINED SPECIFICITY. ENGINEERED RESIDUE IN CHAIN A, HIS 545 TO GLN

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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: 3.53 Å3/Da / Density % sol: 64.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1 MICRO L COMPLEX SOLUTION AND 1 MICRO L RESERVOIR SOLUTION CONSISTING OF 40 % MPD, 0.4 M AMMONIUM FORMATE AND 0.1 M ACETATE BUFFER (PH4.8) AT ...Details: HANGING DROP VAPOR DIFFUSION METHOD BY MIXING 1 MICRO L COMPLEX SOLUTION AND 1 MICRO L RESERVOIR SOLUTION CONSISTING OF 40 % MPD, 0.4 M AMMONIUM FORMATE AND 0.1 M ACETATE BUFFER (PH4.8) AT ROOM TEMPERATURE., pH 4.80

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2004 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9047 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 10.74 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.05 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PT3

1pt3


Resolution: 2.8→47.76 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 106441.89 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 919 10.5 %RANDOM
Rwork0.193 ---
obs0.193 8744 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.0364 Å2 / ksol: 0.307386 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.91 Å20 Å20 Å2
2---4.91 Å20 Å2
3---9.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1006 732 1 87 1826
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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
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_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.371.5
X-RAY DIFFRACTIONc_mcangle_it7.522
X-RAY DIFFRACTIONc_scbond_it8.172
X-RAY DIFFRACTIONc_scangle_it11.112.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 137 10.1 %
Rwork0.322 1225 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA-VVN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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