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- PDB-3sq4: RB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC ri... -

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Basic information

Entry
Database: PDB / ID: 3sq4
TitleRB69 DNA Polymerase Ternary Complex with dTTP Opposite 2AP (GC rich sequence)
Components
  • 5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-3'
  • 5'-D(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)-3'
  • DNA polymerase
KeywordsTRANSFERASE/DNA / 2-Aminopurine / GC rich / 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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsXia, S. / Konigsberg, W.H. / Wang, J.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase.
Authors: Reha-Krantz, L.J. / Hariharan, C. / Subuddhi, U. / Xia, S. / Zhao, C. / Beckman, J. / Christian, T. / Konigsberg, W.
History
DepositionJul 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
T: 5'-D(P*CP*(2PR)P*TP*CP*GP*CP*CP*GP*CP*CP*GP*CP*GP*CP*GP*G)-3'
P: 5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0549
Polymers113,3723
Non-polymers6836
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-68 kcal/mol
Surface area43290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.679, 120.467, 130.992
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: 104507.969 Da / Num. of mol.: 1 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

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


Mass: 4861.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template
#3: DNA chain 5'-D(*CP*GP*CP*GP*CP*GP*GP*CP*GP*GP*CP*GP*(2DA))-3'


Mass: 4002.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer

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Non-polymers , 3 types, 291 molecules

#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 150 mM calcium chloride, 15% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Feb 12, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→88.67 Å / Num. all: 57939 / Num. obs: 54679 / % possible obs: 94.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 2.23→2.28 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→88.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.281 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23837 2911 5.1 %RANDOM
Rwork0.20069 ---
obs0.20263 54679 98.74 %-
all-57939 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.989 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0 Å20 Å2
2--1.79 Å2-0 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.23→88.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7363 591 34 285 8273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1162.05711277
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87724.202376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.024151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.71546
X-RAY DIFFRACTIONr_chiral_restr0.080.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216102
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_it1.42544507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50767309
X-RAY DIFFRACTIONr_scbond_it2.84963740
X-RAY DIFFRACTIONr_scangle_it4.26393966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 175 -
Rwork0.362 3681 -
obs--90.47 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.12380.09760.12640.0492-0.0130.0537-0.2081-0.06950.2642-0.02640.10240.0191-0.0026-0.05670.10560.18540.04720.00290.2730.00420.2339-18.042-2.644-35.186
20.17850.2456-0.15581.3207-0.53120.5090.0080.01270.02940.0435-0.03-0.0737-0.02060.07550.02190.1410.0001-0.01310.09980.02580.094924.7652.437-33.53
30.31940.21240.09970.7764-0.02721.10270.042-0.01080.02130.0984-0.0627-0.00980.0303-0.07740.02080.14040.0016-0.01230.1027-0.00330.045710.348-22.059-14.871
41.03460.7387-0.28390.985-0.05270.2187-0.1450.34420.0605-0.14590.19220.01280.0046-0.1098-0.04730.1732-0.0402-0.01230.20280.03140.0119-3.657-6.667-60.437
50.531-0.077-0.18093.40640.54730.422-0.08820.1098-0.13490.1448-0.02170.0620.0840.02690.10990.17-0.00340.02460.139-0.02050.04919.336-25.913-47.036
60.9623-0.1687-0.67050.92620.22230.5397-0.11940.0131-0.0943-0.07820.11580.09530.00630.06630.00350.2007-0.03320.01860.18-0.02960.1033-9.629-22.861-47.994
72.2664-0.16040.31570.33910.44941.6806-0.115-0.3851-0.14070.02670.12660.04970.0382-0.1874-0.01160.14620.0430.00980.18840.06430.0379-22.337-20.742-28.08
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T3 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A903
4X-RAY DIFFRACTION2A1 - 105
5X-RAY DIFFRACTION2A340 - 389
6X-RAY DIFFRACTION3A106 - 339
7X-RAY DIFFRACTION4A390 - 468
8X-RAY DIFFRACTION4A576 - 706
9X-RAY DIFFRACTION5A469 - 575
10X-RAY DIFFRACTION6A707 - 737
11X-RAY DIFFRACTION7A738 - 901

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