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- PDB-2xo7: Crystal structure of a dA:O-allylhydroxylamine-dC basepair in com... -

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Basic information

Entry
Database: PDB / ID: 2xo7
TitleCrystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
Components
  • 5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3'
  • 5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3'
  • DNA POLYMERASE I
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / EPIGENETICS / PYROSEQUENCING
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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
DNA / DNA (> 10) / : / DNA polymerase I
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMuenzel, M. / Lercher, L. / Mueller, M. / Carell, T.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Chemical Discrimination between Dc and 5Medc Via Their Hydroxylamine Adducts
Authors: Muenzel, M. / Lercher, L. / Mueller, M. / Carell, T.
History
DepositionAug 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Version format compliance
Revision 2.0Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: DNA POLYMERASE I
B: 5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3'
C: 5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0477
Polymers72,6633
Non-polymers3844
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-65.4 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.478, 93.636, 105.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA POLYMERASE I


Mass: 66219.914 Da / Num. of mol.: 1 / Fragment: RESIDUES 297-876
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: C3IXT2, UniProt: E1C9K5*PLUS, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3' / POLYDESOXYRIBONUCLEOTIDE


Mass: 3021.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3' / POLYDESOXYRIBONUCLEOTIDE


Mass: 3422.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY T550 IS S IN OUR SEQUENCE. ...THE ENTRY ABOVE IS NOT FROM STRAIN DSM22, BUT HAS MAXIMUM IDENTITY. ONLY T550 IS S IN OUR SEQUENCE.THE CRYSTALLISED SEQUENCE HAS BEEN MAPPED TO GEOBACILLUS SP. Y412MC52 SINCE THIS IS THE CLOSEST MATCH AVAILABLE (99.8%). AUTHOR HAS PROVIDED A GENBANK ACCESSION CODE FOR THE SEQUENCE WHICH IS YP_003670385.1

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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: 3.26 Å3/Da / Density % sol: 66.3 % / Description: NONE
Crystal growpH: 5.8
Details: 50-55% (NH4)2SO4 3-3.5% MPD 100MM MES, PH 5.8 10MG/ML PROTEIN/DNA 1:3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→43.74 Å / Num. obs: 20704 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.3
Reflection shellResolution: 2.85→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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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: 2.85→43.74 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.727 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1047 5.1 %RANDOM
Rwork0.215 ---
obs0.216 19570 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.17 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å20 Å2
2---3.45 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.85→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 428 20 7 5088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225210
X-RAY DIFFRACTIONr_bond_other_d0.0060.023470
X-RAY DIFFRACTIONr_angle_refined_deg1.3842.0827130
X-RAY DIFFRACTIONr_angle_other_deg0.88738458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8785579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47324.115226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07415869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3261539
X-RAY DIFFRACTIONr_chiral_restr0.0690.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02979
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_it0.471.52898
X-RAY DIFFRACTIONr_mcbond_other0.0891.51160
X-RAY DIFFRACTIONr_mcangle_it0.96724669
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67532312
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9174.52461
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: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 87 -
Rwork0.312 1434 -
obs--99.93 %

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