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- PDB-1mz8: CRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1mz8
TitleCRYSTAL STRUCTURES OF THE NUCLEASE DOMAIN OF COLE7/IM7 IN COMPLEX WITH A PHOSPHATE ION AND A ZINC ION
Components
  • Colicin E7
  • Colicin E7 immunity protein
KeywordsToxin / Hydrolase/protein binding / H-N-H motif / Hydrolase-protein binding COMPLEX
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
PHOSPHATE ION / Colicin-E7 immunity protein / Colicin-E7
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSui, M.J. / Tsai, L.C. / Hsia, K.C. / Doudeva, L.G. / Ku, W.Y. / Han, G.W. / Yuan, H.S.
CitationJournal: PROTEIN SCI. / Year: 2002
Title: Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions
Authors: Sui, M.J. / Tsai, L.C. / Hsia, K.C. / Doudeva, L.G. / Ku, W.Y. / Han, G.W. / Yuan, H.S.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_asym_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S), THAT IS TWO HETERODIMERS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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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)50,2598
Polymers49,9384
Non-polymers3214
Water10,124562
1
A: Colicin E7 immunity protein
B: Colicin E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1294
Polymers24,9692
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Colicin E7 immunity protein
D: Colicin E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1294
Polymers24,9692
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.735, 62.410, 74.137
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
11A-954-

HOH

21C-869-

HOH

31D-1071-

HOH

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Components

#1: Protein Colicin 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) / Gene: cei7 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q03708
#2: Protein Colicin E7


Mass: 15062.104 Da / Num. of mol.: 2 / Fragment: nuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cea7 / Plasmid: pQE30 / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG4000, sodium phosphate, ammonium acetate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMphosphate1droppH6.3
30.35 Mammonium acetate1drop
411 %PEG40001drop
522.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.29004 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29004 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 169490 / Num. obs: 36897 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.061 / Net I/σ(I): 21.7
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5.5 / Num. unique all: 3430 / Rsym value: 0.278 / % possible all: 96.1
Reflection
*PLUS
Num. measured all: 169490 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.278

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7cei

7cei


Resolution: 2→27.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 635436.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3616 10.1 %RANDOM
Rwork0.183 ---
obs0.183 35838 93.6 %-
all-36897 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.4188 Å2 / ksol: 0.390765 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.78 Å20 Å20 Å2
2--2.73 Å20 Å2
3---3.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 12 562 4081
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 536 10.1 %
Rwork0.205 4764 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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