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- PDB-2xhb: Crystal structure of DNA polymerase from Thermococcus gorgonarius... -

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Basic information

Entry
Database: PDB / ID: 2xhb
TitleCrystal structure of DNA polymerase from Thermococcus gorgonarius in complex with hypoxanthine-containing DNA
Components
  • 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
  • DNA POLYMERASE
  • HYPOXANTHINE-CONTAINING DNA
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / REPLICATION / EXONUCLEASE / DNA DAMAGE / EXO MINUS
Function / homology
Function and homology information


exonuclease activity / DNA-templated 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-directed DNA polymerase, family B, multifunctional domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site ...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-directed DNA polymerase, family B, multifunctional 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 polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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: 2.72 Å
AuthorsKillelea, T. / Ghosh, S. / Tan, S.S. / Heslop, P. / Firbank, S.J. / Kool, E.T. / Connolly, B.A.
CitationJournal: Biochemistry / Year: 2010
Title: Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-Ray Crystallography and Non-Hydrogen Bonding Isosteric Base Analogues.
Authors: Killelea, T. / Ghosh, S. / Tan, S.S. / Heslop, P. / Firbank, S.J. / Kool, E.T. / Connolly, B.A.
History
DepositionJun 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE
D: HYPOXANTHINE-CONTAINING DNA
E: 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3284
Polymers101,3053
Non-polymers231
Water39622
1
A: DNA POLYMERASE
D: HYPOXANTHINE-CONTAINING DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5543
Polymers98,5312
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-27.7 kcal/mol
Surface area34010 Å2
MethodPISA
2
E: 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)2,7741
Polymers2,7741
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.450, 98.370, 116.630
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 / TO POL


Mass: 89908.227 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS GORGONARIUS (archaea) / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56689, DNA-directed DNA polymerase
#2: DNA chain HYPOXANTHINE-CONTAINING DNA


Mass: 8622.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'


Mass: 2773.904 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 215 TO ALA
Has protein modificationY
Sequence detailsEXO MINUS MUTANT D215A CHAIN E: IT WAS NOT POSSIBLE TO POSITION THIS DNA IN THE OBSERVED DENSITY ...EXO MINUS MUTANT D215A CHAIN E: IT WAS NOT POSSIBLE TO POSITION THIS DNA IN THE OBSERVED DENSITY WITH ANY CERTAINTY, THUS THE DNA HAS BEEN MODELLED AS THE PHOSPHATE BACKBONE ONLY AND RESIDUES ARE NOT ASSIGNED (ALL ARE GIVEN AS ADENOSINE). THIS DNA IS THOUGHT TO BE A CRYSTALLOGRAPHIC ARTEFACT AND NOT TO BE PHYSIOLOGICALLY RELEVANT.

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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: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE
Crystal growpH: 9 / Details: 0.1M BICINE PH 9.0, 20% PEG6000

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.72→47 Å / Num. obs: 23740 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.8
Reflection shellResolution: 2.72→2.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VWJ

2vwj


Resolution: 2.72→47.01 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.827 / SU B: 9.287 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.967 / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 146-150 AND 374-384 WERE NOT MODELLED OWING TO DISORDER.
RfactorNum. reflection% reflectionSelection details
Rfree0.29455 1229 5.2 %RANDOM
Rwork0.23361 ---
obs0.23676 22478 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---1.2 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.72→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 513 1 22 6485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226656
X-RAY DIFFRACTIONr_bond_other_d0.0010.024468
X-RAY DIFFRACTIONr_angle_refined_deg0.9592.0689111
X-RAY DIFFRACTIONr_angle_other_deg0.783310859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0755738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41323.427286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.708151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3951546
X-RAY DIFFRACTIONr_chiral_restr0.0620.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021335
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_it0.4281.53692
X-RAY DIFFRACTIONr_mcbond_other0.051.51492
X-RAY DIFFRACTIONr_mcangle_it0.80125966
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89232974
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.554.53157
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: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 87 -
Rwork0.314 1657 -
obs--96.41 %

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