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- PDB-3hl8: Crystal structure of exonuclease I in complex with inhibitor BCBP -

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Basic information

Entry
Database: PDB / ID: 3hl8
TitleCrystal structure of exonuclease I in complex with inhibitor BCBP
ComponentsExodeoxyribonuclease I
KeywordsHYDROLASE / EXONUCLEASE / SSB / GENOME MAINTENANCE / DNA DAMAGE / DNA REPAIR / Nuclease
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
Chem-BBP / Exodeoxyribonuclease I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSatyshur, K.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance
Authors: Lu, D. / Bernstein, D.A. / Satyshur, K.A. / Keck, J.L.
History
DepositionMay 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 28, 2014Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 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_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1878
Polymers55,5111
Non-polymers6777
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.823, 91.966, 106.280
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 , 1 types, 1 molecules A

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


Mass: 55510.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2011, cpeA, JW1993, sbcB, xonA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04995, exodeoxyribonuclease I

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Non-polymers , 5 types, 499 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BBP / (5R)-3-tert-butyl-1-(6-chloro-1,3-benzothiazol-2-yl)-4,5-dihydro-1H-pyrazol-5-ol


Mass: 309.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16ClN3OS
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE SEQUENCE ANALYSIS INDICATES THE PRESENCE OF ASP NOT GLU AT SEQUENCE POSITION 472.

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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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mg/mL Protein, 18-27% PEG 4000, 0.1-0.15 M MgCl2, Saturated inhibitor in DMSO soaked 4-5 days, 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: 21-ID-D / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 72323 / Num. obs: 72323 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 34.5
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.69 / Num. unique all: 6559 / % possible all: 85.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
MAR345CCDdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C95

3c95


Resolution: 1.55→26.91 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.904 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20709 3594 5 %RANDOM
Rwork0.17219 ---
all0.1739 68067 --
obs0.1739 68067 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.973 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.5 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.55→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 41 492 4235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223901
X-RAY DIFFRACTIONr_bond_other_d0.0010.022644
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9545316
X-RAY DIFFRACTIONr_angle_other_deg0.87736406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69823.824204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67715635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7751532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
X-RAY DIFFRACTIONr_mcbond_it1.0051.52328
X-RAY DIFFRACTIONr_mcbond_other0.4031.5916
X-RAY DIFFRACTIONr_mcangle_it1.71323774
X-RAY DIFFRACTIONr_scbond_it2.42731573
X-RAY DIFFRACTIONr_scangle_it3.7764.51534
X-RAY DIFFRACTIONr_rigid_bond_restr1.19436545
X-RAY DIFFRACTIONr_sphericity_free4.5393494
X-RAY DIFFRACTIONr_sphericity_bonded2.41336445
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 254 -
Rwork0.209 4556 -
obs--85.12 %

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