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Basic information

Entry
Database: PDB / ID: 3ht3
TitleCrystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP
Components
  • 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'
  • 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'
  • DNA polymerase I, large fragment
KeywordsTRANSFERASE/DNA / protein-DNA complex / DNA polymerase I / DNA replication / DNA-binding / DNA-directed DNA polymerase / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA 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
sucrose / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWu, E.Y. / Beese, L.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism.
Authors: Wu, E.Y. / Beese, L.S.
History
DepositionJun 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase I, large fragment
D: DNA polymerase I, large fragment
B: 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'
C: 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'
E: 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'
F: 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,65317
Polymers144,8886
Non-polymers2,76511
Water17,943996
1
A: DNA polymerase I, large fragment
B: 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'
C: 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7457
Polymers72,4443
Non-polymers1,3014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-19.3 kcal/mol
Surface area28030 Å2
MethodPISA
2
D: DNA polymerase I, large fragment
E: 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'
F: 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,90810
Polymers72,4443
Non-polymers1,4647
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-19.4 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.280, 108.790, 152.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a complex of enzyme and DNA. There are two biological units in the asymmetric unit (chains A,B,C and chains D,E,F).

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Components

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 2684.789 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic oligonucleotide with 2',3'-dideoxy terminus
#3: DNA chain 5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic oligonucleotide

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Protein / Sugars , 2 types, 5 molecules AD

#1: Protein DNA polymerase I, large fragment


Mass: 66055.734 Da / Num. of mol.: 2 / Fragment: Residues 298-876 / Mutation: D598A, V713P
Source method: isolated from a genetically manipulated source
Details: Isolate from Idaho hot spring
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D9N168*PLUS, 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.: 3
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 , 4 types, 1004 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% Saturated ammonium sulfate, 0.1M MES, 2.5% v/v Methylpentanediol, 10mM Magnesium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2MES11
3Methylpentanediol11
4Magnesium sulfate11
5ammonium sulfate12
6MES12
7Methylpentanediol12
8Magnesium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97121 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 2008
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97121 Å / Relative weight: 1
ReflectionResolution: 1.7→46.98 Å / Num. all: 169954 / Num. obs: 169685 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 26.76 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.38
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
SERGUIserguidata collection
XDSdata reduction
REFMAC5.5.0070phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HVI

2hvi


Resolution: 1.7→46.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.309 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24686 7528 4.4 %RANDOM
Rwork0.20974 ---
obs0.2114 169684 100 %-
all-169685 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.552 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.113 Å0.113 Å
Refinement stepCycle: LAST / Resolution: 1.7→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 848 170 996 11306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210664
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3252.09414619
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.30651178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11424.249466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.151151769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.141577
X-RAY DIFFRACTIONr_chiral_restr0.0830.21641
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217668
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6531.55824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24329407
X-RAY DIFFRACTIONr_scbond_it1.91834840
X-RAY DIFFRACTIONr_scangle_it3.1114.55202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 619 -
Rwork0.291 11768 -
obs--100 %

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