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- PDB-3tab: 5-hydroxycytosine paired with dGMP in RB69 gp43 -

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Basic information

Entry
Database: PDB / ID: 3tab
Title5-hydroxycytosine paired with dGMP in RB69 gp43
Components
  • DNA (5'-D(*CP*CP*(5OC)P*GP*GP*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*CP*CP*G)-3')
  • DNA polymerase
KeywordsTransferase/DNA / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZahn, K.E.
CitationJournal: Biochemistry / Year: 2011
Title: The miscoding potential of 5-hydroxycytosine arises due to template instability in the replicative polymerase active site.
Authors: Zahn, K.E. / Averill, A. / Wallace, S.S. / Doublie, S.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jul 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 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_polymer_linkage / 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 / _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
E: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
F: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
B: DNA polymerase
G: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
H: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
C: DNA polymerase
I: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
J: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
D: DNA polymerase
K: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
L: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,08116
Polymers460,69612
Non-polymers3844
Water2,936163
1
A: DNA polymerase
E: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
F: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2704
Polymers115,1743
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-42 kcal/mol
Surface area46740 Å2
MethodPISA
2
B: DNA polymerase
G: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
H: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2704
Polymers115,1743
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-40 kcal/mol
Surface area46360 Å2
MethodPISA
3
C: DNA polymerase
I: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
J: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2704
Polymers115,1743
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-42 kcal/mol
Surface area46070 Å2
MethodPISA
4
D: DNA polymerase
K: DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')
L: DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2704
Polymers115,1743
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-35 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.763, 121.931, 168.912
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA polymerase / / Gp43


Mass: 105069.586 Da / Num. of mol.: 4 / Mutation: D222A, D327A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase
#2: DNA chain
DNA (5'-D(*CP*CP*(5OC)P*GP*GP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')


Mass: 5518.556 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: oligonucleotide
#3: DNA chain
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*CP*CP*G)-3')


Mass: 4585.972 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: oligonucleotide
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% PEG 2000-MME, 100 mM NaOAc, 100 mM MgSO4, 100 mM Hepes, 5% glycerol, 1 mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 15, 2009
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 131768 / Num. obs: 131768 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
CNSrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9 / SU B: 30.821 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28149 12706 9.6 %RANDOM
Rwork0.23199 ---
all0.23678 119040 --
obs0.23678 119040 99.82 %-
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: 92.016 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å23.41 Å2
2--1.4 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29516 2684 20 163 32383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01933262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.871.89845509
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37253610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6724.1541502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4155394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.30515184
X-RAY DIFFRACTIONr_chiral_restr0.060.24706
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02124532
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 862 -
Rwork0.346 8491 -
obs--99.55 %
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)
14.57223.36450.53125.5641.10622.00710.1107-0.75420.7110.42370.05770.1193-0.07760.2894-0.16830.19260.0969-0.14640.8205-0.51660.5068-9.02910.71628.514
26.82163.26321.6318.17073.68091.83480.1823-0.6488-0.29550.42920.0856-0.29250.20170.2699-0.26790.18980.0248-0.16060.7811-0.44030.4371-1.6752.82721.303
35.0244-0.3511.12374.87942.60854.1254-0.06790.1684-0.0929-0.14290.3259-0.40130.1680.4348-0.2580.1350.0124-0.07880.2681-0.13260.2311-22.984-12.7335.231
41.32870.685-0.47255.35354.07414.1364-0.01-0.29570.2767-0.2957-0.31040.3168-0.24950.27580.32040.23310.2285-0.15850.71310.13120.435721.9448.457.637
52.1891-0.08810.34353.01043.1943.5414-0.1115-0.4106-0.14820.19780.1464-0.13390.28770.2482-0.03490.40670.3570.08350.72040.35410.344226.384-8.112.011
62.88071.885-0.268714.196-5.01395.46560.3859-1.155-1.37970.3916-0.4929-0.24112.1429-0.12050.1071.4849-0.0692-0.16861.30320.03371.06297.581-19.75827.592
77.9589-1.0441-0.27650.6671.0132.0624-0.09950.4467-0.3873-0.0832-0.33530.34630.0812-0.76550.43480.3384-0.0217-0.1280.96350.23580.6076-0.289-11.715-22.114
84.7668-4.433-0.26716.18250.21392.04730.11460.57170.0064-0.2296-0.0892-0.080.04140.1571-0.02550.1759-0.0431-0.06270.1909-0.00140.0347-58.57216.73117.375
94.6994-3.1979-0.03065.3617-1.69982.4647-0.20550.0919-0.5384-0.21690.25970.24010.5925-0.0021-0.05420.20440.0033-0.0330.0537-0.03640.1047-63.8738.38725.519
103.92040.6737-0.30352.4413-0.93684.1642-0.0281-0.4235-0.01160.44640.0534-0.18890.36470.8374-0.02540.30060.2375-0.1230.3856-0.06720.1894-39.5160.11242.83
110.9032-0.0426-0.75212.8914-1.64013.12160.00210.15120.0819-0.06280.16680.3465-0.052-0.6434-0.16890.13-0.0237-0.11760.20620.01870.1604-88.50410.02838.766
120.45930.0327-0.30952.7205-1.86182.6758-0.19140.1914-0.2218-0.07560.35140.38680.5979-0.6712-0.160.3576-0.1672-0.01220.2091-0.05220.2212-89.058-6.51745.828
134.4763-0.08660.54774.71840.64966.141-0.09091.018-2.1935-0.62350.1767-0.47782.69351.1833-0.08571.53060.33110.15520.4987-0.42751.1942-66.02-15.2222.034
145.44522.150.69212.7805-0.19373.19370.1007-0.66780.05610.568-0.0794-0.23660.27170.3069-0.02130.46890.117-0.0970.1651-0.04270.1049-62.248-2.37869.703
151.50771.26960.174510.01650.64832.2109-0.0732-0.27180.03440.61880.1957-0.02440.0172-0.0243-0.12260.5451-0.00330.1220.0743-0.02450.1501-75.711-46.85467.895
160.83261.22190.18539.05672.84342.0541-0.0415-0.2278-0.08150.11290.4014-0.432-0.01970.1807-0.35990.4581-0.04250.08230.1496-0.0130.2191-69.089-53.64159.29
174.2189-0.1447-1.62593.00431.24865.2162-0.07440.6812-0.04660.2643-0.23520.60950.6849-1.25670.30960.4816-0.2690.13520.4265-0.05820.3333-90.75-72.98448.781
181.6267-0.7158-1.41522.94812.03863.76870.3981-0.04480.82230.02080.0863-0.2032-0.92390.3116-0.48440.5659-0.18850.20.0818-0.04320.5955-49.797-44.69940.987
191.7224-0.8264-1.2461.72061.20032.50220.2195-0.31180.2610.06790.18-0.322-0.32230.6993-0.39950.2138-0.13110.00910.2373-0.02980.2773-43.885-60.64334.792
204.29220.49411.310314.8757-3.93184.55510.9423-0.9286-1.46331.5415-0.3801-1.10030.91370.5206-0.56220.9949-0.0792-0.39340.42140.15680.8392-57.739-73.90963.904
215.9295-0.16970.53632.00210.40211.92140.04250.54290.1936-0.1926-0.03760.1684-0.0462-0.3367-0.00480.1807-0.0205-0.10440.17890.0950.1335-73.717-71.08117.283
222.5386-1.94090.380110.70931.41033.21530.08111.06830.5015-0.677-0.2539-0.44620.50710.76190.17270.57090.05160.14460.82380.13730.7474-11.184-52.96251.736
235.0759-2.28751.07697.2626-0.81724.22270.3960.23280.6172-0.4485-0.3241-0.13891.16480.7253-0.07190.63720.09060.15160.46620.0290.5087-18.923-58.27260.45
244.44130.66351.17019.1428-2.08062.65430.7924-0.1609-0.42571.9102-0.7183-1.83970.54630.9532-0.07411.89120.421-0.61141.0226-0.13651.1791-0.641-80.40772.145
251.68611.3226-2.69333.369-2.79137.45470.1479-0.36810.56590.47440.1075-0.2206-1.01580.0155-0.25540.5067-0.0217-0.00390.3563-0.26160.9348-36.133-46.37678.781
261.97211.2943-2.04781.6999-2.52674.0456-0.2675-0.18890.18720.18670.1745-0.2593-0.0931-0.37580.09290.5349-0.1011-0.04730.4529-0.25660.6854-43.817-61.39785.449
273.95296.1341.645816.71856.11832.47820.10910.259-0.56010.14-0.1389-0.22870.2158-0.16070.02981.3026-0.1437-0.2210.6068-0.06630.6702-36.528-76.75358.537
289.840.25662.85131.1394-0.02781.2327-0.43070.4163-1.05230.03920.4086-0.228-0.62180.16560.02210.9347-0.0098-0.02250.7816-0.26630.8891-15.427-78.777105.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A340 - 382
3X-RAY DIFFRACTION3A109 - 339
4X-RAY DIFFRACTION4A383 - 468
5X-RAY DIFFRACTION5A573 - 729
6X-RAY DIFFRACTION6A469 - 572
7X-RAY DIFFRACTION7A730 - 903
8X-RAY DIFFRACTION8B1 - 108
9X-RAY DIFFRACTION9B340 - 382
10X-RAY DIFFRACTION10B109 - 339
11X-RAY DIFFRACTION11B383 - 468
12X-RAY DIFFRACTION12B573 - 729
13X-RAY DIFFRACTION13B469 - 572
14X-RAY DIFFRACTION14B730 - 903
15X-RAY DIFFRACTION15C1 - 108
16X-RAY DIFFRACTION16C340 - 382
17X-RAY DIFFRACTION17C109 - 339
18X-RAY DIFFRACTION18C383 - 468
19X-RAY DIFFRACTION19C573 - 729
20X-RAY DIFFRACTION20C469 - 572
21X-RAY DIFFRACTION21C730 - 903
22X-RAY DIFFRACTION22D1 - 108
23X-RAY DIFFRACTION23D340 - 382
24X-RAY DIFFRACTION24D109 - 339
25X-RAY DIFFRACTION25D383 - 468
26X-RAY DIFFRACTION26D573 - 729
27X-RAY DIFFRACTION27D469 - 572
28X-RAY DIFFRACTION28D730 - 903

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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