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- PDB-3h4r: Crystal structure of E. coli RecE exonuclease -

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Basic information

Entry
Database: PDB / ID: 3h4r
TitleCrystal structure of E. coli RecE exonuclease
ComponentsExodeoxyribonuclease 8
KeywordsHYDROLASE / Exonuclease / Recombination / Nuclease
Function / homology
Function and homology information


double-stranded DNA 5'-3' DNA exonuclease activity / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / identical protein binding
Similarity search - Function
Exodeoxyribonuclease 8 / Enterobacterial exodeoxyribonuclease VIII / Putative exodeoxyribonuclease 8, PDDEXK-like domain / PDDEXK-like domain of unknown function (DUF3799) / Lambda Exonuclease; Chain A - #10 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Exodeoxyribonuclease 8
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsBell, C.E. / Zhang, J.
CitationJournal: Structure / Year: 2009
Title: Crystal structure of E. coli RecE protein reveals a toroidal tetramer for processing double-stranded DNA breaks.
Authors: Zhang, J. / Xing, X. / Herr, A.B. / Bell, C.E.
History
DepositionApr 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exodeoxyribonuclease 8


Theoretical massNumber of molelcules
Total (without water)30,4031
Polymers30,4031
Non-polymers00
Water00
1
A: Exodeoxyribonuclease 8

A: Exodeoxyribonuclease 8

A: Exodeoxyribonuclease 8

A: Exodeoxyribonuclease 8


Theoretical massNumber of molelcules
Total (without water)121,6134
Polymers121,6134
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area10840 Å2
ΔGint-59.7 kcal/mol
Surface area41690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.200, 123.200, 67.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Exodeoxyribonuclease 8 / Exodeoxyribonuclease VIII / EXO VIII


Mass: 30403.252 Da / Num. of mol.: 1 / Fragment: C-terminal domain: UNP residues 606-866 / Mutation: P658L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1350, JW1344, recE / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI)
References: UniProt: P15032, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters

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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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30-42% Glycerol, 100 mM DL-malic acid, pH 7.0, 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: 0.97929 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2007
RadiationMonochromator: Kohzu HLD-4 Diamond(111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 13172 / Num. obs: 13172 / % possible obs: 99.4 % / Redundancy: 23.5 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 23.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHENIXmodel building
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→45.43 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 3811437.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.313 656 5 %RANDOM
Rwork0.29 ---
obs0.29 13172 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.5675 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 97.3 Å2
Baniso -1Baniso -2Baniso -3
1--25.55 Å20 Å20 Å2
2---25.55 Å20 Å2
3---51.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.99 Å0.83 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 0 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.473 112 5.2 %
Rwork0.476 2028 -
obs--99.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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