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- PDB-1fxx: THE STRUCTURE OF EXONUCLEASE I SUGGESTS HOW PROCESSIVITY IS ACHIEVED -

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Basic information

Entry
Database: PDB / ID: 1fxx
TitleTHE STRUCTURE OF EXONUCLEASE I SUGGESTS HOW PROCESSIVITY IS ACHIEVED
ComponentsEXONUCLEASE I
KeywordsHYDROLASE / alpha-beta domain / SH3-like domain / DnaQ superfamily
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
PHOSPHATE ION / Exodeoxyribonuclease I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBreyer, W.A. / Matthews, B.W.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of Escherichia coli exonuclease I suggests how processivity is achieved.
Authors: Breyer, W.A. / Matthews, B.W.
History
DepositionSep 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_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

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Assembly

Deposited unit
A: EXONUCLEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7224
Polymers55,5111
Non-polymers2113
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.410, 84.410, 298.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

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Components

#1: Protein EXONUCLEASE I / EXODEOXYRIBONUCLEASE I


Mass: 55510.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P04995, exodeoxyribonuclease I
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 25

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.85 - 2.0M Na/K Phosphate, 20% v/v Glycerol, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.85-2.0 MNa,K phosphate1reservoir
220 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 25722 / Num. obs: 24672 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.267 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 462433
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 1225 -RANDOM
Rwork0.2038 ---
all0.2202 25660 --
obs0.2202 24603 95.9 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 12 102 3842
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.236 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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