- PDB-4a1n: Human Mitochondrial endo-exonuclease -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4a1n
Title
Human Mitochondrial endo-exonuclease
Components
NUCLEASE EXOG, MITOCHONDRIAL
Keywords
HYDROLASE
Function / homology
Function and homology information
Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex / mitochondrion ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex / mitochondrion / nucleus / metal ion binding Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1250 / EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1250 / EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 37981.941 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-368 Source method: isolated from a genetically manipulated source Details: CLONING ARTIFACT GLU330VAL / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CH2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THERE IS A GLU330VAL MUTATION IN THE PROTEIN SEQUENCE. THE SIDE CHAIN WAS NOT VISIBLE IN THE ...THERE IS A GLU330VAL MUTATION IN THE PROTEIN SEQUENCE. THE SIDE CHAIN WAS NOT VISIBLE IN THE ELECTRON DENSITY. WE BELIEVE THIS IS A CLONING ARTIFACT.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.39 Å3/Da / Density % sol: 63.76 % / Description: NONE
Resolution: 2.8→44.68 Å / Cor.coef. Fo:Fc: 0.9278 / Cor.coef. Fo:Fc free: 0.8949 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.268 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CL NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2375. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=2. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CL NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2375. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=2. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2249
653
5 %
RANDOM
Rwork
0.1752
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obs
0.1776
13052
100 %
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Displacement parameters
Biso mean: 37.17 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.2868 Å2
0 Å2
0 Å2
2-
-
0.2868 Å2
0 Å2
3-
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-0.5737 Å2
Refine analyze
Luzzati coordinate error obs: 0.283 Å
Refinement step
Cycle: LAST / Resolution: 2.8→44.68 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2299
0
4
67
2370
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2364
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.14
3207
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1083
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
59
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
343
HARMONIC
5
X-RAY DIFFRACTION
t_it
2364
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
1
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.45
X-RAY DIFFRACTION
t_other_torsion
3.1
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
303
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
2745
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→3.02 Å / Total num. of bins used: 7
Rfactor
Num. reflection
% reflection
Rfree
0.2439
133
5 %
Rwork
0.1927
2528
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all
0.1954
2661
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obs
-
-
100 %
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