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- PDB-4uqg: A new bio-isosteric base pair based on reversible bonding -

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Basic information

Entry
Database: PDB / ID: 4uqg
TitleA new bio-isosteric base pair based on reversible bonding
Components
  • 5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3'
  • 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3'
  • DNA POLYMERASE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / UNNATURAL BASE PAIR
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / DNA / DNA polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTomas-Gamasa, M. / Serdjukov, S. / Su, M. / Mueller, M. / Carell, T.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2015
Title: "Post-it" type connected DNA created with a reversible covalent cross-link.
Authors: Tomas-Gamasa, M. / Serdjukow, S. / Su, M. / Muller, M. / Carell, T.
History
DepositionJun 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references / Other / Refinement description
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_validate_polymer_linkage / Item: _diffrn_detector.type
Revision 1.4Feb 20, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / pdbx_database_proc ...citation / pdbx_database_proc / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE
B: 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3'
C: 5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0228
Polymers72,2953
Non-polymers7275
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-56.7 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.442, 93.996, 105.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3' / POLYDEOXYRIBONUCLEOTIDE B


Mass: 3025.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: LINK TO CHAIN C VIA RESIDUE SAY / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3' / POLYDEOXYRIBONUCLEOTIDE C


Mass: 3121.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: LINK TO CHAIN B VIA RESIDUE T0T / Source: (synth.) synthetic construct (others)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein DNA POLYMERASE / DNA POLYMERASE I FRAGMENT


Mass: 66148.828 Da / Num. of mol.: 1 / Fragment: POLYMERASE DOMAIN, RESIDUES 2-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Strain: DSM 22 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E1C9K5, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 214 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSYNTHETIC CONSTRUCT

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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: 3.28 Å3/Da / Density % sol: 62.57 % / Description: NONE
Crystal growDetails: 46-49% AMMONIUM SULFATE, 2-3% MPD, 100MM MES PH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→70.16 Å / Num. obs: 59562 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.05
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.59 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XY5

2xy5


Resolution: 2→70.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.904 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21116 2937 4.9 %RANDOM
Rwork0.17814 ---
obs0.17977 56624 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å20 Å2
2---2.23 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2→70.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4538 411 43 210 5202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195127
X-RAY DIFFRACTIONr_bond_other_d0.0070.024729
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.917035
X-RAY DIFFRACTIONr_angle_other_deg1.138310857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0724.159214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49115811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4781536
X-RAY DIFFRACTIONr_chiral_restr0.1060.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025486
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.93.2122317
X-RAY DIFFRACTIONr_mcbond_other2.8883.2112316
X-RAY DIFFRACTIONr_mcangle_it3.5474.7972895
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.3623.8262810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 222 -
Rwork0.294 3928 -
obs--95.07 %

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