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- PDB-2v6e: protelomerase TelK complexed with substrate DNA -

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Basic information

Entry
Database: PDB / ID: 2v6e
Titleprotelomerase TelK complexed with substrate DNA
Components
  • (TELRL) x 2
  • PROTELEMORASE
KeywordsHYDROLASE / HAIRPIN TELOMERE / RESOLVASE / PROTELOMERASE / DNA DISTORTION
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #2040 / Helix Hairpins - #3180 / de novo design (two linked rop proteins) - #270 / Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / hpI Integrase; Chain A / de novo design (two linked rop proteins) / Helix Hairpins ...Arc Repressor Mutant, subunit A - #2040 / Helix Hairpins - #3180 / de novo design (two linked rop proteins) - #270 / Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / hpI Integrase; Chain A / de novo design (two linked rop proteins) / Helix Hairpins / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
VANADATE ION / DNA / DNA (> 10) / Protelomerase
Similarity search - Component
Biological speciesKLEBSIELLA PHAGE PHIKO2 (virus)
PHAGE N15 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.2 Å
AuthorsAihara, H. / Huang, W.M. / Ellenberger, T.
CitationJournal: Mol.Cell / Year: 2007
Title: An Interlocked Dimer of the Protelomerase Telk Distorts DNA Structure for the Formation of Hairpin Telomeres
Authors: Aihara, H. / Huang, W.M. / Ellenberger, T.
History
DepositionJul 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTELEMORASE
B: PROTELEMORASE
C: TELRL
D: TELRL
E: TELRL
F: TELRL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,7148
Polymers155,4846
Non-polymers2302
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-13.3 kcal/mol
Surface area70760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)157.973, 157.973, 90.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.00046, 1, -0.00028), (-1, 0.00046, 0.0003), (-0.0003, -0.00028, -1)
Vector: 0.04012, -0.05718, 93.17863)

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Components

#1: Protein PROTELEMORASE / PROTELOMERASE TELK538


Mass: 64239.176 Da / Num. of mol.: 2
Fragment: C-TERMINALLY TRUNCATED ACTIVE RESOLVASE, RESIDUES 1-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PHAGE PHIKO2 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6UAV6
#2: DNA chain TELRL


Mass: 7770.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TARGET SITE FOR TELK / Source: (synth.) PHAGE N15 (virus)
#3: DNA chain TELRL


Mass: 5732.751 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TARGET SITE FOR TELK / Source: (synth.) PHAGE N15 (virus)
#4: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4

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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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 36966 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 73.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.2→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1680 4.5 %RANDOM
Rwork0.2554 ---
obs0.2554 36209 97.4 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL / Bsol: 37.9419 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 57.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.094 Å20 Å20 Å2
2--7.094 Å20 Å2
3----14.188 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8284 1792 6 0 10082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008279
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.43158
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.2→3.23 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.353 58 5.6 %
Rwork0.306 983 -
obs--95 %

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