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- PDB-1fsj: CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1fsj
TitleCRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN
ComponentsCOLICIN E9
KeywordsHYDROLASE / zinc containing enzyme / HNH-motif
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 / 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/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 ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / 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 / His-Me finger superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Colicin-E9
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsKuhlmann, U.C. / Pommer, A.J. / Moore, G.R. / James, R. / Kleanthous, C. / Hemmings, A.M.
Citation
Journal: To be Published
Title: Structure of the E9 DNase domain in comparison with the inhibited structure of the E9 DNase/Im9 complex
Authors: Kuhlmann, U.C. / Pommer, A.J. / Moore, G.R. / James, R. / Kleanthous, C. / Hemmings, A.M.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Specificity in protein-protein interactions: The structural basis for dual recognition in endonuclease colicin-immunity protein complexes
Authors: Kuhlmann, U.C. / Pommer, A.J. / Moore, G.R. / James, R. / Kleanthous, C.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: 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
B: COLICIN E9
C: COLICIN E9
D: COLICIN E9
E: COLICIN E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,12212
Polymers60,4804
Non-polymers6428
Water5,711317
1
B: COLICIN E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2803
Polymers15,1201
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: COLICIN E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2803
Polymers15,1201
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: COLICIN E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2803
Polymers15,1201
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: COLICIN E9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2803
Polymers15,1201
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.120, 82.960, 113.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological active enzyme is probably a monomer

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Components

#1: Protein
COLICIN E9


Mass: 15120.021 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN OF E9 COLICIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET21D (PRJ353) / Production host: Escherichia coli (E. coli) / References: UniProt: P09883, deoxyribonuclease I
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 30% (w/v) PEG 5000, 0.1M sodium-acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 49812 / Num. obs: 49775 / % possible obs: 97.6 % / Observed criterion σ(F): 2.7 / Redundancy: 5.2 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.135 / Num. unique all: 5140 / % possible all: 94.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 1.8→25 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2417 -random
Rwork0.189 ---
all-49641 --
obs-48351 95.1 %-
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4205 0 24 317 4546
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.5

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