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- PDB-1v15: CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1v15
TitleCRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DSDNA (RESOLUTION 2.4A)
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: 2.4 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 / 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 / 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.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.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

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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)80,15620
Polymers79,63312
Non-polymers5238
Water2,378132
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)20,0395
Polymers19,9083
Non-polymers1312
Water543
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)20,0395
Polymers19,9083
Non-polymers1312
Water543
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)20,0395
Polymers19,9083
Non-polymers1312
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)20,0395
Polymers19,9083
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.145, 123.310, 110.531
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
11D-2022-

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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE HIS 551 ALA THIS PLASMID-CODED BACTERICIDAL PROTEIN IS AN ENDONUCLEASE ACTIVE ON ...ENGINEERED RESIDUE HIS 551 ALA 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: 36.4 %
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: 0.9645
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9645 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25215 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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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: 2.4→74.54 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.876 / SU B: 31.98 / SU ML: 0.369 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.786 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.329 1286 5.1 %RANDOM
Rwork0.242 ---
obs0.246 23929 99.9 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 68.74 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å20 Å20 Å2
2---1.91 Å20 Å2
3---4.91 Å2
Refinement stepCycle: LAST / Resolution: 2.4→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 1168 8 132 5261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8732.2327382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27824.402184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26715740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3551528
X-RAY DIFFRACTIONr_chiral_restr0.1980.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023667
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22172
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.160.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3861.52557
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67524009
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.03233512
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5894.53373
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 112
Rwork0.295 1722
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)
18.46591.5301-1.29285.35662.35673.88680.04210.95232.0961-0.77620.27120.2622-0.79350.4197-0.31330.3821-0.1556-0.0783-0.33370.71510.68582.6842139.354512.6266
210.0003-1.79960.00582.54951.06924.1547-0.19651.1470.3022-0.10470.2007-0.52890.15210.6256-0.0042-0.2229-0.17740.04360.14430.1134-0.368328.7391109.26111.7101
36.2748-2.60042.01798.352-0.30794.60380.093-0.633-1.4420.51790.21640.20910.45490-0.3094-0.2021-0.00050.0529-0.28170.2519-0.27961.3798242.7462
410.61622.44520.64344.44090.40843.8504-0.1419-0.69650.16060.3933-0.2595-1.0315-0.39940.40880.4014-0.2153-0.063-0.1691-0.06140.1481-0.203629.2756113.238642.5404
58.9769-4.2554-2.18517.40180.66328.3731-0.28230.11061.54420.49360.0002-0.5996-0.45170.51860.2821-0.0654-0.1496-0.1408-0.27760.31190.238111.7349128.537619.8311
68.91794.11433.53569.39331.19763.7084-0.19320.2712-0.47190.4292-0.0348-0.4672-0.0430.25470.228-0.3017-0.14730.1309-0.24610.0013-0.376516.7435100.314819.3301
78.06234.75681.98844.4257-1.56439.2597-0.39730.2757-0.9552-0.46280.0467-1.1781-0.3670.64470.3506-0.2887-0.05180.0659-0.32340.0744-0.35611.970594.145835.4347
811.3082-0.6132-2.51847.9994-2.78373.88580.1357-0.09251.8023-0.0406-0.346-0.1874-0.6337-0.40780.2103-0.14080.0659-0.1629-0.3169-0.03270.022317.0168122.459735.5823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 131
2X-RAY DIFFRACTION2B1 - 134
3X-RAY DIFFRACTION3C3 - 131
4X-RAY DIFFRACTION4D2 - 134
5X-RAY DIFFRACTION5E2 - 8
6X-RAY DIFFRACTION6F9 - 16
7X-RAY DIFFRACTION7G3 - 8
8X-RAY DIFFRACTION8H9 - 16

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