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- PDB-4dsj: Crystal structure of fragment DNA polymerase I from Bacillus stea... -

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Basic information

Entry
Database: PDB / ID: 4dsj
TitleCrystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, dGTP and Calcium
Components
  • DNA
  • DNA polymerase
  • dGTP
KeywordsTRANSFERASE/DNA / DNA polymerase / polymerization fidelity / calcium cation / pyrophosphorolysis / purine selectivity / blunt end extension / base stacking / DNA synthesis / 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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsGan, J.H. / Abdur, R. / Liu, H.H. / Sheng, J. / Caton-Willians, J. / Soares, A.S. / Huang, Z.
CitationJournal: To be Published
Title: Biochemical and structural insights into the fidelity of bacillus stearothermophilus DNA polymerase
Authors: Gan, J.H. / Abdur, R. / Liu, H.H. / Sheng, J. / Caton-Willians, J. / Soares, A.S. / Huang, Z.
History
DepositionFeb 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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: DNA polymerase
B: DNA polymerase
C: DNA
D: dGTP
E: DNA
F: dGTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,2089
Polymers145,6206
Non-polymers5873
Water1629
1
A: DNA polymerase
C: DNA
D: dGTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3976
Polymers72,8103
Non-polymers5873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-44 kcal/mol
Surface area28030 Å2
MethodPISA
2
B: DNA polymerase
E: DNA
F: dGTP


Theoretical massNumber of molelcules
Total (without water)72,8103
Polymers72,8103
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-21 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.016, 112.070, 229.450
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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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase


Mass: 66101.766 Da / Num. of mol.: 2 / Fragment: RESIDUES 298-876 / Mutation: A598D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: D9N168, UniProt: E1C9K5*PLUS, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA


Mass: 3687.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized DNA
#3: DNA chain dGTP


Mass: 3020.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized dGTP

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Non-polymers , 3 types, 12 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Tris-Bris (pH 6.5), 28% PEG2000, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2011 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→114.73 Å / Num. all: 36088 / Num. obs: 32948 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rsym value: 0.091 / Net I/σ(I): 15.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 3548 / Rsym value: 0.367 / % possible all: 89.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3ht3

3ht3


Resolution: 2.86→114.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 43.389 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2771 3260 9.9 %RANDOM
Rwork0.21256 ---
obs0.21758 29531 89.76 %-
all-36088 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.974 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---4.73 Å20 Å2
3---5.06 Å2
Refinement stepCycle: LAST / Resolution: 2.86→114.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9266 890 33 9 10198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210476
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5492.08614353
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30251155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72724.242462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.993151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2721576
X-RAY DIFFRACTIONr_chiral_restr0.0950.21609
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217588
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_it0.4421.55771
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8629309
X-RAY DIFFRACTIONr_scbond_it1.35834705
X-RAY DIFFRACTIONr_scangle_it2.3334.55042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.865→2.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 182 -
Rwork0.331 1754 -
obs--72.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69820.30390.04341.53720.00680.2168-0.0319-0.03840.0001-0.08120.01960.06950.0664-0.02370.01230.22180.0209-0.01480.3662-0.00430.202426.082415.704654.2098
21.71520.12710.01151.8998-0.47880.90940.20480.0732-0.1708-0.2566-0.2247-0.06590.1690.13420.01990.51740.04680.00090.170.00110.01948.8183-2.75272.6319
32.52060.4841-0.72080.59740.75452.4346-0.18510.32580.0457-0.23320.2136-0.00610.28840.1294-0.02850.6447-0.00080.01470.5871-0.04980.313437.677421.249942.7042
41.74210.4657-0.92962.5045-2.25812.36470.03980.1033-0.24030.04090.0685-0.0067-0.27220.0225-0.10830.5433-0.05870.05340.5883-0.05940.37937.172321.617443.616
51.671-1.6584-1.89291.91112.39735.04650.33920.2470.3636-0.0984-0.0986-0.13880.3538-0.6438-0.24060.8333-0.00730.06650.7311-0.07170.661945.454312.865910.3621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A298 - 876
2X-RAY DIFFRACTION2B298 - 876
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D21 - 30
5X-RAY DIFFRACTION5E1 - 12

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