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- PDB-4jrq: Crystal structure of E. coli Exonuclease I in complex with a 5cy-... -

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Basic information

Entry
Database: PDB / ID: 4jrq
TitleCrystal structure of E. coli Exonuclease I in complex with a 5cy-dA13 oligonucleotide
Components
  • 5cy-dA13
  • Exodeoxyribonuclease I
KeywordsHYDROLASE/DNA / Exonuclease / DnaQ superfamily / 3'-5' ssDNA 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
DNA / DNA (> 10) / Exodeoxyribonuclease I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 / 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 / _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-dA13
D: 5cy-dA13
A: Exodeoxyribonuclease I
B: Exodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,52313
Polymers118,6594
Non-polymers8659
Water00
1
C: 5cy-dA13
A: Exodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0029
Polymers59,3292
Non-polymers6727
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-84 kcal/mol
Surface area21510 Å2
MethodPISA
2
D: 5cy-dA13
B: Exodeoxyribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5214
Polymers59,3292
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-32 kcal/mol
Surface area21610 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-131 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.252, 91.252, 162.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.990368, 0.123546, -0.062516), (0.128878, 0.987567, -0.090008), (0.050619, -0.097198, -0.993977)9.09326, 1.28966, 34.81419

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Components

#1: DNA chain 5cy-dA13


Mass: 4480.370 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 / 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

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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: 2.84 Å3/Da / Density % sol: 56.76 %
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: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.666
11-H, K, -L20.334
ReflectionResolution: 3→20 Å / Num. all: 25103 / Num. obs: 25103 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rmerge(I) obs: 0.65 / Net I/σ(I): 16.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

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

1fxx


Resolution: 3→19.98 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 19.242 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24466 1270 4.8 %RANDOM
Rwork0.21833 ---
all0.21967 25103 --
obs0.21967 25103 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.534 Å2
Baniso -1Baniso -2Baniso -3
1-34.87 Å20 Å20 Å2
2--34.87 Å20 Å2
3----69.74 Å2
Refinement stepCycle: LAST / Resolution: 3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7020 546 45 0 7611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0197869
X-RAY DIFFRACTIONr_bond_other_d0.0010.026808
X-RAY DIFFRACTIONr_angle_refined_deg0.7411.87810902
X-RAY DIFFRACTIONr_angle_other_deg0.762315492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5285913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69623.645332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1631544
X-RAY DIFFRACTIONr_chiral_restr0.0460.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021910
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 105 -
Rwork0.251 1823 -
obs--100 %

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