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- PDB-1v14: Crystal Structure of the Colicin E9, mutant His103Ala, in complex... -

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Basic information

Entry
Database: PDB / ID: 1v14
TitleCrystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A)
Components
  • 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
  • COLICIN E9
KeywordsHYDROLASE / HOMING ENDONUCLEASES / COLICIN / HNH MOTIF / BETA-BETA-ALPHA METAL 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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMate, M.J. / Kleanthous, C.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases
Authors: Mate, M.J. / Kleanthous, C.
#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.M. / James, R. / Kleanthous, C.
History
DepositionApr 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 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 / pdbx_struct_special_symmetry / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN E9
B: COLICIN E9
C: COLICIN E9
D: COLICIN E9
E: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
F: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
G: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
H: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
I: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
J: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
K: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
L: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,77818
Polymers79,63312
Non-polymers1466
Water59433
1
A: COLICIN E9
E: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
F: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9575
Polymers19,9083
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: COLICIN E9
G: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
H: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9324
Polymers19,9083
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: COLICIN E9
I: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
J: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9575
Polymers19,9083
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: COLICIN E9
K: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
L: 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9324
Polymers19,9083
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.946, 124.442, 111.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2001-

HOH

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Components

#1: Protein
COLICIN E9


Mass: 15052.951 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 450-582 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PTRC 99A (PRJ352) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09883, deoxyribonuclease I
#2: DNA chain
5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3'


Mass: 2427.605 Da / Num. of mol.: 8 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE ALA 103 HIS THIS PLASMID-CODED BACTERICIDAL PROTEIN IS AN ENDONUCLEASE ACTIVE ON ...ENGINEERED RESIDUE ALA 103 HIS THIS PLASMID-CODED BACTERICIDAL PROTEIN IS AN ENDONUCLEASE ACTIVE ON BOTH SINGLE- AND DOUBLE-STRANDED DNA

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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 Å3/Da / Density % sol: 37 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9465
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9465 Å / Relative weight: 1
ReflectionResolution: 2.9→70 Å / Num. obs: 14593 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 11.4
Reflection shellResolution: 2.9→3.12 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMV

1emv


Resolution: 2.9→74.54 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.871 / SU B: 52.69 / SU ML: 0.459 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.306 734 5 %RANDOM
Rwork0.215 ---
obs0.219 13856 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2---0.81 Å20 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 1136 6 33 5328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225513
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.2167637
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85724.372199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.75615800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4461532
X-RAY DIFFRACTIONr_chiral_restr0.1410.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023824
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22246
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.261.52658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.48824223
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.733573
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1854.53414
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 54
Rwork0.303 1013
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.14551.6817-0.96094.29080.2762.8333-0.06970.56641.5291-0.4044-0.00340.256-0.57060.14110.07320.1361-0.1432-0.225-0.16280.41030.473248.17379.097168.371
28.90672.1477-0.05666.5980.30772.9232-0.2113-1.2681-0.13510.46620.3042-0.8144-0.10140.8599-0.0928-0.22580.179-0.07130.30760.0123-0.356875.357877.106943.3288
34.9259-0.677-1.83386.64320.02113.83210.1187-0.67531.20180.2580.1790.1818-0.6998-0.1454-0.2978-0.06190.0087-0.0127-0.2652-0.2197-0.132744.5942104.013842.8816
48.6971-2.74320.26715.59710.12283.8709-0.05190.4668-0.0893-0.4509-0.3502-1.04260.22580.54670.4021-0.2757-0.03230.0894-0.1240.1019-0.253575.742172.73712.5576
56.2947-3.3169-1.44274.42351.50311.9208-0.6760.18071.14910.28060.0498-0.2223-0.24410.51360.6262-0.0927-0.1736-0.1907-0.30640.26010.036357.515866.606975.1671
66.5558-0.4343-3.96592.20730.17822.85130.0402-0.23160.6451-0.46140.15820.0371-0.3340.3226-0.1984-0.23690.0456-0.147-0.244-0.0702-0.414663.212885.743335.9847
74.91163.6097-1.51642.9962-1.34085.1731-0.21220.20420.5469-0.4074-0.03190.54040.087-0.42610.2441-0.20910.0611-0.0773-0.4688-0.0729-0.26135.291291.516735.8277
86.9117-0.24741.85461.1552-0.62981.2381-0.1551-0.2282-1.24550.2995-0.0776-0.04970.39570.02020.2327-0.2151-0.07690.1605-0.3454-0.051-0.135463.338463.576919.8433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 132
2X-RAY DIFFRACTION2B1 - 132
3X-RAY DIFFRACTION3C2 - 132
4X-RAY DIFFRACTION4D4 - 132
5X-RAY DIFFRACTION5E3 - 8
6X-RAY DIFFRACTION6F9 - 16
7X-RAY DIFFRACTION7G3 - 8
8X-RAY DIFFRACTION8H9 - 16

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