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- PDB-4hcc: The zinc ion bound form of crystal structure of E.coli ExoI-ssDNA... -

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Basic information

Entry
Database: PDB / ID: 4hcc
TitleThe zinc ion bound 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 / HYDROLASE-DNA complex
Function / homology
Function and homology information


exodeoxyribonuclease I / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / 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 / PHOSPHATE ION / DNA / DNA (> 10) / Exodeoxyribonuclease I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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
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)119,36318
Polymers118,1904
Non-polymers1,17314
Water36020
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)59,6048
Polymers59,0952
Non-polymers5096
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-92 kcal/mol
Surface area22750 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)59,76010
Polymers59,0952
Non-polymers6658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-89 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.037, 108.692, 158.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#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)

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Non-polymers , 5 types, 34 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The crystals grew in 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, 5 mM phenol, then soaked in the solution consisted of precipitant ...Details: The crystals grew in 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, 5 mM phenol, then soaked in the solution consisted of precipitant solution and 20 mM zinc chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. all: 23347 / Num. obs: 23141 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.091 / Χ2: 1.189 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-37.10.43611451.252199.6
3-3.067.20.36311381.268199.6
3.06-3.117.10.33211501.261199.5
3.11-3.187.20.2711361.268199.4
3.18-3.257.10.23311251.297199.5
3.25-3.327.10.21411321.351199.5
3.32-3.47.20.17611561.257199.6
3.4-3.570.15611421.28199.7
3.5-3.67.10.1311411.169199.2
3.6-3.727.10.11911451.192199.4
3.72-3.8570.111391.046199.7
3.85-470.08911511.062199.4
4-4.186.90.08211601.239199.1
4.18-4.46.80.07611491.158199.1
4.4-4.686.70.06711541.083199.6
4.68-5.046.70.06711661.067199.5
5.04-5.546.70.06611641.121199.5
5.54-6.346.60.06412041.181199.6
6.34-7.966.40.05311971.088198.8
7.96-305.60.04412471.1196.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HCB

4hcb


Resolution: 2.96→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0 / SU B: 16.616 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2448 1188 5.1 %RANDOM
Rwork0.1849 ---
obs0.188 23099 98.49 %-
all-23347 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.34 Å2 / Biso mean: 62.8263 Å2 / Biso min: 27.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2---1.35 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7538 414 57 20 8029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0198221
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.90811264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2985924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55723.734399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.186151240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7841560
X-RAY DIFFRACTIONr_chiral_restr0.0770.21202
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216244
LS refinement shellResolution: 2.96→3.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 75 -
Rwork0.254 1315 -
all-1390 -
obs--89.27 %

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