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- PDB-4e0z: Protelomerase tela R205A covalently complexed with substrate DNA -

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Basic information

Entry
Database: PDB / ID: 4e0z
TitleProtelomerase tela R205A covalently complexed with substrate DNA
Components
  • DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')
  • DNA (5'-D(*TP*CP*A*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
  • Protelomerase
KeywordsDNA BINDING PROTEIN/DNA / PROTELEMORASE / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Helix Hairpins - #1780 / Telomere resolvase / Telomere resolvase ResT / Telomere resolvase ResT superfamily / Telomere resolvase ResT/TelK catalytic domain / hpI Integrase; Chain A / Helix Hairpins / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / Protelomerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsShi, K. / Aihara, H.
CitationJournal: Plos Biol. / Year: 2013
Title: An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.
Authors: Shi, K. / Huang, W.M. / Aihara, H.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Feb 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')
D: DNA (5'-D(*TP*CP*A*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0448
Polymers62,3533
Non-polymers6915
Water4,612256
1
A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')
D: DNA (5'-D(*TP*CP*A*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
hetero molecules

A: Protelomerase
C: DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')
D: DNA (5'-D(*TP*CP*A*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,08816
Polymers124,7076
Non-polymers1,38110
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15190 Å2
ΔGint-67 kcal/mol
Surface area35490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.273, 120.390, 58.719
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protelomerase


Mass: 52562.055 Da / Num. of mol.: 1 / Mutation: R205A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: telA, Atu2523 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CWV1

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*AP*TP*AP*AP*TP*AP*AP*CP*AP*AP*TP*A)-3')


Mass: 3951.639 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*CP*A*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*AP*TP*G)-3')


Mass: 5839.804 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 261 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5% (w/v) PEG 4000, 10mM Tris-HCl, 300mM NaCl , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 25104 / Num. obs: 25104 / % possible obs: 73.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→35.689 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1186 4.99 %
Rwork0.1909 --
obs0.1941 23775 82.64 %
all-23792 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8829 Å2-0 Å2-0.6509 Å2
2---3.5115 Å2-0 Å2
3---4.3945 Å2
Refinement stepCycle: LAST / Resolution: 2.42→35.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 590 41 256 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113286
X-RAY DIFFRACTIONf_angle_d1.5784560
X-RAY DIFFRACTIONf_dihedral_angle_d21.9741257
X-RAY DIFFRACTIONf_chiral_restr0.086498
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4201-2.53020.2442820.1791588X-RAY DIFFRACTION46
2.5302-2.66350.2883930.22482025X-RAY DIFFRACTION59
2.6635-2.83030.2961100.25262471X-RAY DIFFRACTION73
2.8303-3.04880.38281540.26243048X-RAY DIFFRACTION89
3.0488-3.35540.31251870.21843337X-RAY DIFFRACTION98
3.3554-3.84040.2421790.17763383X-RAY DIFFRACTION99
3.8404-4.83660.21061760.14613359X-RAY DIFFRACTION99
4.8366-35.69330.20342050.17243378X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 20.7701 Å / Origin y: -11.232 Å / Origin z: 3.2541 Å
111213212223313233
T0.2225 Å2-0.0145 Å2-0.0207 Å2-0.2641 Å20.0191 Å2--0.307 Å2
L4.0515 °2-0.4929 °20.0298 °2-3.399 °20.0121 °2--0.6611 °2
S-0.0029 Å °-0.1698 Å °0.0972 Å °0.1344 Å °0.0419 Å °-0.8623 Å °-0.0101 Å °0.1512 Å °-0.0067 Å °
Refinement TLS groupSelection details: all

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