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- PDB-2djh: Crystal structure of the carboxy-terminal ribonuclease domain of ... -

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Basic information

Entry
Database: PDB / ID: 2djh
TitleCrystal structure of the carboxy-terminal ribonuclease domain of Colicin E5
ComponentsColicin-E5
KeywordsHYDROLASE / alpha/beta protein
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYajima, S. / Inoue, S. / Ogawa, T. / Nonaka, T. / Ohsawa, K. / Masaki, H.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction
Authors: Yajima, S. / Inoue, S. / Ogawa, T. / Nonaka, T. / Ohsawa, K. / Masaki, H.
History
DepositionApr 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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_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

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Assembly

Deposited unit
A: Colicin-E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3783
Polymers12,7231
Non-polymers6552
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.190, 48.720, 62.580
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 / Fragment


Mass: 12723.011 Da / Num. of mol.: 1 / Fragment: C-terminal ribonuclease domain, residues 2-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBR328 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1
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


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.747624 Å3/Da / Density % sol: 29.618711 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M ammonium sulfate, 20mM TrisCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→38.3 Å / Num. all: 9473 / Num. obs: 9397 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.17 / Num. unique all: 936 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2dfx; chain_id E

2dfx


Resolution: 1.9→26.46 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 395 -random
Rwork0.198 ---
all0.199 7466 --
obs0.199 7399 100 %-
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms749 0 42 105 896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.9→2.09 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.214 115 6.3 %
Rwork0.252 1723 -
obs-1214 -

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