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- PDB-3lzj: RB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,... -

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Basic information

Entry
Database: PDB / ID: 3lzj
TitleRB69 DNA Polymerase (Y567A) ternary complex with dCTP Opposite 7,8-Dihydro-8-oxoguanine
Components
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
  • DNA (5'-D(P*TP*CP*AP*(8OG)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA polymerase / replication fidelity / 7 / 8-dihydro-8-oxoguanine / Polymerase-DNA-dNTP ternary complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / 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 / Monooxygenase ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / 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 / Monooxygenase / 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsWang, M. / Beckman, J. / Blaha, G. / Wang, J. / Konigsberg, W.H.
CitationJournal: Biochemistry / Year: 2010
Title: Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine .
Authors: Beckman, J. / Wang, M. / Blaha, G. / Wang, J. / Konigsberg, W.H.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA (5'-D(P*TP*CP*AP*(8OG)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
P: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7168
Polymers114,0723
Non-polymers6435
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-53 kcal/mol
Surface area43500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.394, 121.089, 122.857
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, 1 molecules A

#1: Protein DNA polymerase / / Gp43


Mass: 104563.047 Da / Num. of mol.: 1 / Mutation: D222A, D327A, Y567A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Plasmid: pET 21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(P*TP*CP*AP*(8OG)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5557.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA strand
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA strand

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Non-polymers , 3 types, 573 molecules

#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293.15 K / Method: micro-batch vapor-diffusion / pH: 6.5
Details: 150 mM CaCl2, 14%(w/v) PEG 350 monomethyl ether (MME), and 100 mM Na Cacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 65594 / % possible obs: 90.7 % / Observed criterion σ(I): 1.03 / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 1.03 / % possible all: 70.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.05→38.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.864 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AUTHORS NOTED THAT TLS MADE SOMEWHAT LARGE CONTRIBUTIONS TO LOWER R AND FREE R-FACTORS BY 4-6% DURING REFINEMENT WITH THE PROGRAM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AUTHORS NOTED THAT TLS MADE SOMEWHAT LARGE CONTRIBUTIONS TO LOWER R AND FREE R-FACTORS BY 4-6% DURING REFINEMENT WITH THE PROGRAM REFMAC, AND THAT BULK SOLVENT MODELS DIFFERED SUBSTANTIALLY WITH AND WITHOUT TLS WHEN THE STRUCTURE FACTORS WERE CALCULATED USING SFCHECK.
RfactorNum. reflection% reflectionSelection details
Rfree0.25065 3317 5.1 %RANDOM
Rwork0.20462 ---
obs0.20696 62176 90.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.084 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å20 Å20 Å2
2--3.61 Å20 Å2
3----6.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7367 634 32 568 8601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2582.06111354
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69424.122376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.712151351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4731547
X-RAY DIFFRACTIONr_chiral_restr0.0790.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216143
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_it1.43744515
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29667321
X-RAY DIFFRACTIONr_scbond_it2.78263792
X-RAY DIFFRACTIONr_scangle_it3.98494032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 152 -
Rwork0.3 3484 -
obs--69.22 %
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)
11.5007-0.0677-0.62181.2126-0.37140.413-0.30670.4025-0.1705-0.21830.28930.21740.1555-0.32880.01740.2534-0.1029-0.01240.4418-0.0370.7101-19.8125.74-23.685
21.0563-1.0014-0.21994.387-1.13912.26080.1520.03620.2548-1.0705-0.4834-1.21230.61250.45470.33150.42870.17880.39710.15130.13451.005221.8350.168-26.479
31.1967-0.0207-0.22722.1699-2.13943.669-0.10350.1275-0.0715-1.2721-0.2191-0.54591.04280.01830.32260.88470.08420.36930.09050.01660.80067.08622.859-47.521
40.7867-0.4331-0.22421.44550.01111.0202-0.059-0.19770.04280.15440.0859-0.08520.0797-0.1941-0.0270.1246-0.01650.00280.2231-0.01530.6277-5.79712.76-0.196
50.3277-0.10040.14095.1406-0.70731.4981-0.0815-0.0280.12840.0742-0.0372-0.2644-0.30820.02190.11880.1445-0.01190.03570.1369-0.0090.72156.93630.516-15.393
61.72961.10120.88581.80920.1652.13610.03080.03960.0827-0.13350.1889-0.044-0.0039-0.2484-0.21980.15970.04160.01050.2233-0.00470.6466-11.66927.375-14.072
72.20680.1091-0.71212.50710.51662.4224-0.15310.56260.1238-0.70360.19840.3569-0.005-0.6828-0.04540.293-0.1095-0.12460.46560.13090.6188-24.69722.454-33.878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T1 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION2A1 - 105
4X-RAY DIFFRACTION2A340 - 389
5X-RAY DIFFRACTION3A106 - 339
6X-RAY DIFFRACTION4A390 - 468
7X-RAY DIFFRACTION4A576 - 706
8X-RAY DIFFRACTION5A469 - 575
9X-RAY DIFFRACTION6A707 - 737
10X-RAY DIFFRACTION7A738 - 901

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