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- PDB-3vj7: Crystal structure of the carboxy-terminal ribonuclease domain of ... -

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Basic information

Entry
Database: PDB / ID: 3vj7
TitleCrystal structure of the carboxy-terminal ribonuclease domain of Colicin E5 R33Q mutant
ComponentsColicin-E5
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


RNA nuclease activity / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium
Similarity search - Function
Colicin E5 C-terminal ribonuclease domain (CRD) / Colicin E5 ribonuclease domain / Colicin E5 ribonuclease domain superfamily / Colicin E5 ribonuclease domain / Colicin D/E5 nuclease domain superfamily / YaeB-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3PD / 2'-DEOXYURIDINE 3'-MONOPHOSPHATE / Colicin-E5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYajima, S. / Inoue, S. / Fushinobu, S. / Ogawa, T. / Hidaka, M. / Masaki, H.
CitationJournal: J.Biochem. / Year: 2012
Title: Identification of the catalytic residues of sequence-specific and histidine-free ribonuclease colicin E5
Authors: Inoue-Ito, S. / Yajima, S. / Fushinobu, S. / Nakamura, S. / Ogawa, T. / Hidaka, M. / Masaki, H.
History
DepositionOct 13, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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-E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3493
Polymers12,6941
Non-polymers6552
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.688, 49.450, 64.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Colicin-E5


Mass: 12693.945 Da / Num. of mol.: 1
Fragment: C-terminal ribonuclease domain, UNP residues 66-180
Mutation: R33Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: col / Production host: Escherichia coli (E. coli)
References: UniProt: P18000, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-3PD / 2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE / 2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-UM3 / 2'-DEOXYURIDINE 3'-MONOPHOSPHATE / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulfate, 20mM TrisCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 28, 1999
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 4583 / Num. obs: 4574 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
DIP-2030data collection
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DJH

2djh


Resolution: 2.3→39.27 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 207 4.6 %RANDOM
Rwork0.23801 ---
obs0.23888 4307 99.25 %-
all-4340 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.526 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---0.08 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 42 54 826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8332.0021065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.365593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44625.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98315124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.948155
X-RAY DIFFRACTIONr_chiral_restr0.1140.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021602
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_it1.5091.5467
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.642760
X-RAY DIFFRACTIONr_scbond_it2.3013326
X-RAY DIFFRACTIONr_scangle_it3.5344.5305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 14 -
Rwork0.233 301 -
obs--99.06 %

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