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- PDB-3kd1: Closed binary complex of an RB69 gp43 fingers domain mutant compl... -

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Basic information

Entry
Database: PDB / ID: 3kd1
TitleClosed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.
Components
  • DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / gp43 / polymerase / HCMV / human cytomegalovirus / acyclovir / acyclic guanosine / foscavir / foscarnet / phosphonoformic acid / DNA replication / DNA-binding / DNA-directed DNA polymerase / Exonuclease / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / 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
DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 2.66 Å
AuthorsZahn, K.E. / Doublie, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase.
Authors: Zahn, K.E. / Tchesnokov, E.P. / Gotte, M. / Doublie, S.
History
DepositionOct 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jan 11, 2017Group: Other
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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_conn_type.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 1.6Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
P: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')
E: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6024
Polymers115,5783
Non-polymers241
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-30 kcal/mol
Surface area44740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.485, 121.657, 131.538
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: DNA chain DNA (5'-D(*CP*GP*TP*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')


Mass: 5492.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized
#2: DNA chain DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(4DG))-3')


Mass: 4278.780 Da / Num. of mol.: 1 / Fragment: Acyclic GMP terminated primer DNA / Source method: obtained synthetically / Details: Oligonucleotide was chemically synthesized
#3: Protein DNA polymerase / / Gp43


Mass: 105806.359 Da / Num. of mol.: 1
Fragment: RB69 gp43 exo- chimera containing elements from the fingers domain of the human cytomegalovirus DNA polymerase.
Mutation: D222A V478W F479V N480S I557M N558A R559L L561V I562T I563C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, RB69 gp43 / Plasmid: pPR-IBA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q38087, DNA-directed DNA polymerase
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5% PEG 20000, 0.1M sodium acetate pH 5, 0.1M magnesium acetate, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03315 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2009
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. all: 36963 / Num. obs: 36963 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 17.7
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.24 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0054refinement
CNSrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: isomorphous replacement
Starting model: PDB entry 1IH7

1ih7


Resolution: 2.66→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 22.55 / SU ML: 0.249 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24826 3570 9.7 %RANDOM
Rwork0.20796 ---
obs0.2119 33291 99.96 %-
all-33291 --
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: 41.056 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--0.34 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.66→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7379 648 1 321 8349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228286
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9162.0611333
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5055904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21424.182373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.168151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0941545
X-RAY DIFFRACTIONr_chiral_restr0.0630.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216121
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_it0.1611.54516
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.30827320
X-RAY DIFFRACTIONr_scbond_it0.41233770
X-RAY DIFFRACTIONr_scangle_it0.754.54013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 274 -
Rwork0.368 2398 -
obs--99.89 %
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)
11.05390.4516-0.00189.2309-2.69362.56580.0832-0.01380.09480.231-0.096-0.653-0.1140.17770.01280.024-0.0384-0.0330.16280.01640.218428.39362.07834.941
21.36892.4475-0.6515.4849-0.90711.43-0.09520.0866-0.1416-0.19610.0374-0.4311-0.01730.24180.05780.04520.0004-0.02340.12230.00810.118119.46755.16828.919
31.3510.58330.20651.56650.00171.69480.1103-0.16310.05960.3838-0.1336-0.08210.1198-0.14020.02330.2243-0.0305-0.09240.1055-0.01160.05298.96536.54851.448
42.59741.4107-0.31242.44640.27881.3382-0.08390.25130.2641-0.22350.1482-0.0965-0.2366-0.0265-0.06430.15460.03970.0260.15850.07290.081.64760.919.156
51.63480.89480.14541.84090.43660.7038-0.06690.4403-0.0726-0.24310.0908-0.05420.0058-0.0884-0.0240.07470.01270.01390.21040.00520.0115-4.55744.6615.221
61.4816-0.23870.13158.03031.14321.1718-0.00060.246-0.37490.23670.1004-0.10730.24570.0436-0.09970.08540.0221-0.02740.1466-0.03090.12429.68930.79318.374
72.44330.48020.77281.64190.7322.440.0577-0.2599-0.0650.3965-0.14220.16160.1528-0.42320.08460.1141-0.04410.04590.16550.00930.0311-22.90938.12436.049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 108
2X-RAY DIFFRACTION2E340 - 382
3X-RAY DIFFRACTION3E109 - 339
4X-RAY DIFFRACTION4E383 - 468
5X-RAY DIFFRACTION5E573 - 729
6X-RAY DIFFRACTION6E469 - 572
7X-RAY DIFFRACTION7E730 - 905

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