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- PDB-4jrp: Structure of E. coli Exonuclease I in complex with a 5cy-dT13 oli... -

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Basic information

Entry
Database: PDB / ID: 4jrp
TitleStructure of E. coli Exonuclease I in complex with a 5cy-dT13 oligonucleotide
Components
  • 5cy-dT13
  • Exodeoxyribonuclease I
KeywordsHYDROLASE/DNA / DNA REPAIR / DnaQ superfamily / EXONUCLEASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


exodeoxyribonuclease I / DNA replication termination / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / 5'-deoxyribose-5-phosphate lyase activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / DNA repair / magnesium ion binding
Similarity search - Function
Helix Hairpins - #1240 / Exonuclease ExoI, domain 3 / Exonuclease ExoI, domain 2 / Exodeoxyribonuclease I, C-terminal / Exodeoxyribonuclease I / Exonuclease I, SH3-like domain / Exonuclease I, C-terminal alpha-helical domain / Exonuclease I, SH3-like domain superfamily / Exonuclease C-terminal / Exonuclease I (ExoI) SH3-like domain profile. ...Helix Hairpins - #1240 / Exonuclease ExoI, domain 3 / Exonuclease ExoI, domain 2 / Exodeoxyribonuclease I, C-terminal / Exodeoxyribonuclease I / Exonuclease I, SH3-like domain / Exonuclease I, C-terminal alpha-helical domain / Exonuclease I, SH3-like domain superfamily / Exonuclease C-terminal / Exonuclease I (ExoI) SH3-like domain profile. / Exonuclease I (ExoI) C-terminal domain profile. / Oligoribonuclease / PX Domain / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Monooxygenase / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / DNA / DNA (> 10) / Exodeoxyribonuclease I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBell, C.E.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.
Authors: Korada, S.K. / Johns, T.D. / Smith, C.E. / Jones, N.D. / McCabe, K.A. / Bell, C.E.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _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
C: 5cy-dT13
D: 5cy-dT13
A: Exodeoxyribonuclease I
B: Exodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,03822
Polymers118,4244
Non-polymers1,61318
Water7,296405
1
C: 5cy-dT13
A: Exodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,90110
Polymers59,2122
Non-polymers6898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-93 kcal/mol
Surface area22150 Å2
MethodPISA
2
D: 5cy-dT13
B: Exodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,13712
Polymers59,2122
Non-polymers92510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-116 kcal/mol
Surface area23460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13640 Å2
ΔGint-249 kcal/mol
Surface area42000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.300, 91.300, 159.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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DNA chain / Protein , 2 types, 4 molecules CDAB

#1: DNA chain 5cy-dT13


Mass: 4363.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis
#2: Protein Exodeoxyribonuclease I / Exonuclease I / DNA deoxyribophosphodiesterase / dRPase


Mass: 54848.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 6His-thrombin tag / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: sbcB, cpeA, xonA, b2011, JW1993 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: P04995, exodeoxyribonuclease I

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Non-polymers , 5 types, 423 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5 % 2-propanol, 25% glycerol, 1.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2012 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.768
11K, H, -L20.232
ReflectionResolution: 1.95→36.6 Å / Num. all: 89174 / Num. obs: 89174 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2 / % possible all: 93.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.7.0029refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXX

1fxx


Resolution: 1.95→36.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.4 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25909 4852 5.2 %RANDOM
Rwork0.21315 ---
obs0.21543 89174 99.11 %-
all-89174 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.392 Å2
Baniso -1Baniso -2Baniso -3
1-8.02 Å20 Å20 Å2
2--8.02 Å20 Å2
3----16.03 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 590 87 405 8474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.90811421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97223.76391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.771151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5421560
X-RAY DIFFRACTIONr_chiral_restr0.090.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216287
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 339 -
Rwork0.484 6167 -
obs--93.01 %

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