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- PDB-4udm: Crystal structure of Im3 in complex with Y52A mutant of E3RNase -

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Basic information

Entry
Database: PDB / ID: 4udm
TitleCrystal structure of Im3 in complex with Y52A mutant of E3RNase
Components
  • COLICIN-E3
  • COLICIN-E3 IMMUNITY PROTEIN
KeywordsTRANSLATION / ANTIBIOTIC / ANTIMICROBIAL / BACTERIOCIN / BACTERIOCIN IMMUNITY / ENDONUCLEASE / HYDROLASE / INHIBITION / NUCLEASE / PROTEIN-PROTEIN INTERACTIONS / RIBONUCLEASE / RIBOSOME INACTIVATION / TOXIN
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / transmembrane transporter binding / killing of cells of another organism / tRNA binding ...negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / transmembrane transporter binding / killing of cells of another organism / tRNA binding / rRNA binding / lyase activity / defense response to bacterium / extracellular region
Similarity search - Function
Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / Colicin, receptor domain ...Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / 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 / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
Colicin E3 / Colicin E3 immunity protein
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsSharma, A. / Kleanthous, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Consequences of Inducing Intrinsic Disorder in a High-Affinity Protein-Protein Interaction.
Authors: Papadakos, G. / Sharma, A. / Lancaster, L.E. / Bowen, R. / Kaminska, R. / Leech, A.P. / Walker, D. / Redfield, C. / Kleanthous, C.
History
DepositionDec 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN-E3 IMMUNITY PROTEIN
B: COLICIN-E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7866
Polymers20,6312
Non-polymers1564
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-27 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.854, 92.854, 76.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein COLICIN-E3 IMMUNITY PROTEIN / COLICIN-E3 CHAIN B / IMME3 / MICROCIN-E3 IMMUNITY PROTEIN / IMMUNITY PROTEIN


Mass: 9910.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P02984
#2: Protein COLICIN-E3 / COLICIN-E3 A CHAIN / RIBONUCLEASE / COLICIN E3


Mass: 10720.021 Da / Num. of mol.: 1 / Fragment: RIBONUCLEASE DOMAIN, UNP RESIDUES 456-551 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P00646
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.39 Å3/Da / Density % sol: 48.65 %
Description: MOLECULAR REPLACEMENT WAS CARRIED OUT USING THE INDIVIDUAL CHAINS FROM 1E44.PDB
Crystal growpH: 6.5 / Details: 0.1M BIS-TRIS PH 6.5, 50MM CACL2,30%PEG550MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9835
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9835 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 30491 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 88.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 2.97→3.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 3.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E44

1e44


Resolution: 2.96→38.47 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.101 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21378 767 5 %RANDOM
Rwork0.18425 ---
obs0.18569 14625 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.428 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.96→38.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1451 0 4 4 1459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221528
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9522063
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91624.87882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.678157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7691.5906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.49821451
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9243622
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2474.5610
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: 2.962→3.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 63 -
Rwork0.292 1047 -
obs--98.32 %

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