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- PDB-4dwp: SeMet protelomerase tela covalently complexed with substrate DNA -

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Basic information

Entry
Database: PDB / ID: 4dwp
TitleSeMet protelomerase tela covalently complexed with substrate DNA
Components
  • DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-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 / SAD / Resolution: 2.35 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
DepositionFeb 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Protelomerase
C: DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
D: DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1764
Polymers63,8543
Non-polymers3221
Water6,251347
1
A: Protelomerase
C: DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
D: DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3')
hetero molecules

A: Protelomerase
C: DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')
D: DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3538
Polymers127,7086
Non-polymers6442
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14840 Å2
ΔGint-55 kcal/mol
Surface area36050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.851, 119.766, 65.984
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

21C-135-

HOH

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Components

#1: Protein Protelomerase


Mass: 53445.379 Da / Num. of mol.: 1
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
#2: DNA chain DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)-3')


Mass: 4560.024 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3')


Mass: 5848.818 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
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: 3.46 Å3/Da / Density % sol: 64.4 %
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: 14-ID-B / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2009
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: 2.3→50 Å / Num. all: 31866 / Num. obs: 31866 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 2.3→2.34 Å / % possible all: 45.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→40.838 Å / SU ML: 0.28 / σ(F): 0 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1450 4.94 %
Rwork0.1889 --
obs0.1908 29358 81.28 %
all-29358 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.454 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.199 Å20 Å2-1.2042 Å2
2--0.3841 Å20 Å2
3----0.5831 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 634 17 347 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093330
X-RAY DIFFRACTIONf_angle_d1.2754639
X-RAY DIFFRACTIONf_dihedral_angle_d22.4561281
X-RAY DIFFRACTIONf_chiral_restr0.075509
X-RAY DIFFRACTIONf_plane_restr0.005485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3502-2.43420.2149670.21061397X-RAY DIFFRACTION41
2.4342-2.53170.27811030.21031887X-RAY DIFFRACTION56
2.5317-2.64690.24911130.23282197X-RAY DIFFRACTION64
2.6469-2.78640.29611210.22582454X-RAY DIFFRACTION71
2.7864-2.96090.27771760.23822898X-RAY DIFFRACTION85
2.9609-3.18940.29041770.22953334X-RAY DIFFRACTION98
3.1894-3.51030.21891720.18343421X-RAY DIFFRACTION99
3.5103-4.01780.22041780.17183402X-RAY DIFFRACTION100
4.0178-5.06050.18391650.14543449X-RAY DIFFRACTION99
5.0605-40.84430.19621780.18683469X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -31.3488 Å / Origin y: 3.2584 Å / Origin z: 27.7841 Å
111213212223313233
T0.0945 Å20.0239 Å2-0.0489 Å2-0.1335 Å2-0.0266 Å2--0.0694 Å2
L3.1071 °20.35 °2-0.5594 °2-3.5711 °2-0.0022 °2--0.8608 °2
S0.1451 Å °0.2354 Å °-0.0138 Å °-0.1209 Å °-0.0959 Å °0.7532 Å °-0.0215 Å °-0.0888 Å °-0.0339 Å °
Refinement TLS groupSelection details: all

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