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- PDB-4hcb: The metal-free form of crystal structure of E.coli ExoI-ssDNA complex -

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Basic information

Entry
Database: PDB / ID: 4hcb
TitleThe metal-free form of crystal structure of E.coli ExoI-ssDNA complex
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Exodeoxyribonuclease I
KeywordsHYDROLASE/DNA / DnaQ family / Exonuclease C-terminal family / 3'-5' 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 I SH3-like domain / 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 I SH3-like domain / 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: 2 Å
AuthorsQiu, R. / Wei, J. / Lou, T. / Liu, M. / Ji, C. / Gong, W.
CitationJournal: To be published
Title: The structures of Escherichia coli exonuclease I in complex with the single strand DNA
Authors: Qiu, R. / Lou, T. / Wei, J. / Liu, M. / Gu, S. / Tang, R. / Ji, C. / Gong, W.
History
DepositionSep 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_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: Exodeoxyribonuclease I
B: Exodeoxyribonuclease I
C: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
D: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,23515
Polymers118,1904
Non-polymers1,04511
Water8,935496
1
A: Exodeoxyribonuclease I
C: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5717
Polymers59,0952
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-63 kcal/mol
Surface area23160 Å2
MethodPISA
2
B: Exodeoxyribonuclease I
D: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6638
Polymers59,0952
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-45 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.544, 107.289, 157.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exodeoxyribonuclease I / Exonuclease I / DNA deoxyribophosphodiesterase / dRPase


Mass: 55381.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5alpha / Gene: b2011, cpeA, JW1993, sbcB, xonA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04995, exodeoxyribonuclease I
#2: DNA chain DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3713.524 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The ssDNA samples were synthesized with 3'-phosphoryl modification (PAGE purified)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS ASP FOR E.COLI STRAIN DH5ALPHA

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.65-1.68 M ammonium sulfate, 6.5-6.8% v/v 2-propanol, 0.1 M sodium citrate tribasic dihydrate pH 6.0 and 5 mM phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 72101 / Num. obs: 71457 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.083 / Χ2: 1.312 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.078.30.29770941.008199.7
2.07-2.158.30.23370931.134199.8
2.15-2.258.40.18871021.298199.9
2.25-2.378.30.15571121.406199.9
2.37-2.528.40.13171311.474199.7
2.52-2.718.40.11271611.396199.6
2.71-2.998.40.09371531.382199.5
2.99-3.428.30.08271861.15199.4
3.42-4.318.20.07671511.51198.1
4.31-507.80.05272741.361195.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C95

3c95


Resolution: 2→37.663 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8556 / SU ML: 0.5 / σ(F): 1.34 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 3605 5.05 %RANDOM
Rwork0.1828 ---
obs0.1849 71392 98.59 %-
all-72101 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.013 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 100.59 Å2 / Biso mean: 32.88 Å2 / Biso min: 13 Å2
Baniso -1Baniso -2Baniso -3
1-2.1914 Å20 Å2-0 Å2
2--2.3433 Å2-0 Å2
3----4.5347 Å2
Refinement stepCycle: LAST / Resolution: 2→37.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 481 58 496 8530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088320
X-RAY DIFFRACTIONf_angle_d1.00211421
X-RAY DIFFRACTIONf_chiral_restr0.071226
X-RAY DIFFRACTIONf_plane_restr0.0041411
X-RAY DIFFRACTIONf_dihedral_angle_d15.7213083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02660.28231270.19762213234085
2.0266-2.05440.24541240.199826072731100
2.0544-2.08370.26121310.194126122743100
2.0837-2.11480.28311470.188226062753100
2.1148-2.14790.23831400.193126012741100
2.1479-2.18310.26421370.185325932730100
2.1831-2.22070.24891460.190926152761100
2.2207-2.26110.23111550.183226112766100
2.2611-2.30460.24021500.181825872737100
2.3046-2.35160.24491510.186826162767100
2.3516-2.40270.23521340.185926342768100
2.4027-2.45860.26911380.191125882726100
2.4586-2.52010.25551400.194726182758100
2.5201-2.58820.29631310.206426282759100
2.5882-2.66440.25151430.195826162759100
2.6644-2.75030.23531350.198526522787100
2.7503-2.84860.23921340.20592624275899
2.8486-2.96260.26091570.19726212778100
2.9626-3.09740.22381280.20162633276199
3.0974-3.26060.21541240.1912650277499
3.2606-3.46480.2181380.17852641277999
3.4648-3.7320.21251420.17082616275899
3.732-4.10720.18381410.15872629277098
4.1072-4.70060.21290.15522634276397
4.7006-5.91850.19841340.1772635276996
5.9185-37.6630.19081490.18642707285695

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