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- PDB-2vwj: Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray ... -

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Basic information

Entry
Database: PDB / ID: 2vwj
TitleUracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography.
Components
  • 5'-D(*AP*AP*UP*GP*GP*AP*GP*AP*CP*GP *GP*CP*TP*TP*TP*TP*GP*CP*CP*GP*TP*GP*TP*C)-3'
  • DNA POLYMERASE
KeywordsDNA REPLICATION / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / TRANSFERASE / EXONUCLEASE / DNA-BINDING / DNA POLYMERASE / URACIL / ARCHAEA / NUCLEASE / HYDROLASE / DNA REPAIR
Function / homology
Function and homology information


exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain ...DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesTHERMOCOCCUS GORGONARIUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsFirbank, S.J. / Wardle, J. / Heslop, P. / Lewis, R.J. / Connolly, B.A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Uracil Recognition in Archaeal DNA Polymerases Captured by X-Ray Crystallography.
Authors: Firbank, S.J. / Wardle, J. / Heslop, P. / Lewis, R.J. / Connolly, B.A.
History
DepositionJun 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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

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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(*AP*AP*UP*GP*GP*AP*GP*AP*CP*GP *GP*CP*TP*TP*TP*TP*GP*CP*CP*GP*TP*GP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0595
Polymers97,9412
Non-polymers1173
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-10.1 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.700, 161.910, 221.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DNA POLYMERASE / / TGO POLYMERASE DNA COMPLEX / TO POL


Mass: 89936.305 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS GORGONARIUS (archaea) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56689, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*AP*AP*UP*GP*GP*AP*GP*AP*CP*GP *GP*CP*TP*TP*TP*TP*GP*CP*CP*GP*TP*GP*TP*C)-3'


Mass: 8005.138 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 215 TO ALA
Sequence detailsMUTATION OF D215 TO ALANINE TO REMOVE EXONUCLEASE ACTIVITY.

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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: 4.5 Å3/Da / Density % sol: 76 % / Description: NONE
Crystal growpH: 8.3 / Details: 0.2M TRIPOTASSIUM CITRATE PH8.3, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: SI (111) DOUBLE CRYSTAL MONOCHROMATOR. KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 2.78→30 Å / Num. obs: 45193 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGO

1tgo


Resolution: 2.78→67.73 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.645 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2296 5.1 %RANDOM
Rwork0.227 ---
obs0.229 42895 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.83 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å20 Å2
2--4.01 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.78→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6077 478 3 1 6559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226751
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4072.0629235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10423.562292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.83151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.261545
X-RAY DIFFRACTIONr_chiral_restr0.0910.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024943
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.22858
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2206
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6221.53771
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18926090
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.50733055
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6874.53145
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: 2.78→2.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.397 153
Rwork0.352 3148

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