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- PDB-2xy5: Crystal structure of an artificial salen-copper basepair in compl... -

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Basic information

Entry
Database: PDB / ID: 2xy5
TitleCrystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
Components
  • 5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3'
  • 5'-D(*GP*AP*CP*CP*SAYP*TP*CP*CP*CP*TP)-3'
  • DNA POLYMERASE I
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / SYNTHETIC BIOLOGY / METAL BASEPAIR / REPLICATION / SALEN COMPLEX
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
surcrose isoform / COPPER (I) ION / ETHANE-1,2-DIAMINE / DNA / DNA polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKaul, C. / Mueller, M. / Wagner, M. / Schneider, S. / Carell, T.
CitationJournal: Nature Chem. / Year: 2011
Title: Reversible Bond Formation Enables the Replication and Amplification of a Crosslinking Salen Complex as an Orthogonal Base Pair.
Authors: Kaul, C. / Mueller, M. / Wagner, M. / Schneider, S. / Carell, T.
History
DepositionNov 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references / Other
Revision 1.2May 30, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,33211
Polymers72,3643
Non-polymers9688
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-80 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.171, 93.469, 105.591
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*CP*SAYP*TP*CP*CP*CP*TP)-3' / POLYDESOXYRIBONUCLEOTIDE


Mass: 2951.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*GP*GP*GP*AP*SAYP*GP*GP*TP*CP)-3' / POLYDESOXYRIBONUCLEOTIDE


Mass: 3121.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein DNA POLYMERASE I


Mass: 66290.992 Da / Num. of mol.: 1
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(DE3) / References: UniProt: E1C9K5, DNA-directed DNA polymerase
#4: Polysaccharide alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranose / surcrose isoform


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / 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: surcrose isoform
DescriptorTypeProgram
DFrufa2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2a_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 190 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#8: Chemical ChemComp-EDN / ETHANE-1,2-DIAMINE / ETHYLENEDIAMINE


Mass: 60.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H8N2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsEDN: REACTS WITH SAY AND CU1 TO YIELD A CROSSLINK OF TWO DNA STRANDS. 2 H2O ARE RELEASED. MRD: 2- ...EDN: REACTS WITH SAY AND CU1 TO YIELD A CROSSLINK OF TWO DNA STRANDS. 2 H2O ARE RELEASED. MRD: 2-METHYL-2,4-PENTANEDIOL ALSO KNOWN AS HEXYLENE GLYCOL SAY: 2'-DEOXY-1'-(3-HYDROXY-4-FORMYLPHENYL)RIBOSE-5'-MONOPHOSPHATE
Sequence detailsTHE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY THR 550 IS SER IN OUR SEQUENCE.

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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: 3.3 Å3/Da / Density % sol: 62.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.3785
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3785 Å / Relative weight: 1
ReflectionResolution: 2.22→93.47 Å / Num. obs: 43840 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.9
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U45

1u45


Resolution: 2.22→67.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.938 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 2189 5 %RANDOM
Rwork0.19314 ---
obs0.1952 41587 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.675 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å20 Å2
2---1.26 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.22→67.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 404 56 183 5215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225169
X-RAY DIFFRACTIONr_bond_other_d0.0060.023371
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.0827093
X-RAY DIFFRACTIONr_angle_other_deg0.9043.0018204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03724.279222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11315822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6971536
X-RAY DIFFRACTIONr_chiral_restr0.0790.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215423
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
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_it0.6851.52910
X-RAY DIFFRACTIONr_mcbond_other0.1451.51164
X-RAY DIFFRACTIONr_mcangle_it1.32724676
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06332259
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3164.52415
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: 2.219→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 157 -
Rwork0.232 2985 -
obs--100 %

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