- PDB-1ako: EXONUCLEASE III FROM ESCHERICHIA COLI -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1ako
Title
EXONUCLEASE III FROM ESCHERICHIA COLI
Components
EXONUCLEASE III
Keywords
NUCLEASE / EXONUCLEASE / AP-ENDONUCLEASE / DNA REPAIR
Function / homology
Function and homology information
: / exodeoxyribonuclease III / exonuclease activity / endonuclease activity / DNA repair / DNA damage response / DNA binding / metal ion binding / cytosol Similarity search - Function
Exodeoxyribonuclease III-like / AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase ...Exodeoxyribonuclease III-like / AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.7→1.78 Å / Mean I/σ(I) obs: 1.5 / % possible all: 62
Reflection
*PLUS
Num. measured all: 199757 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 62 %
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Processing
Software
Name
Version
Classification
PHASES
phasing
X-PLOR
3.8
modelbuilding
X-PLOR
3.8
refinement
XENGEN
V. 1.3
datareduction
XENGEN
V. 1.3
datascaling
X-PLOR
3.8
phasing
Refinement
Method to determine structure: MIR / Resolution: 1.7→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0 Details: AN OVERALL BULK SOLVENT CORRECTION WAS APPLIED USNG X-PLOR V3.8 AND LOW RESOLUTION DATA INCLUDED TO 20 ANGSTROMS THE THREE RAMACHANDRAN OUTLIER RESIDUES (TYR 63, GLU 114, AND SER 178) ALL ...Details: AN OVERALL BULK SOLVENT CORRECTION WAS APPLIED USNG X-PLOR V3.8 AND LOW RESOLUTION DATA INCLUDED TO 20 ANGSTROMS THE THREE RAMACHANDRAN OUTLIER RESIDUES (TYR 63, GLU 114, AND SER 178) ALL RESIDE IN LOOPS ON THE DNA BINDING SURFACE OF THE ENZYME AND MAY PLAY ROLES IN ENZYME FUNCTION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.202
2769
10 %
RANDOM
Rwork
0.169
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-
-
obs
0.169
27067
86.9 %
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Displacement parameters
Biso mean: 17.7 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2183
0
0
190
2373
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.008
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
1.391
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
24.19
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.181
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
1.47
X-RAY DIFFRACTION
x_mcangle_it
2.23
X-RAY DIFFRACTION
x_scbond_it
3.37
X-RAY DIFFRACTION
x_scangle_it
5.25
LS refinement shell
Resolution: 1.7→1.78 Å / Total num. of bins used: 8
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