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- PDB-4fjm: RB69 DNA polymerase ternary complex with dCTP/dA -

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Basic information

Entry
Database: PDB / ID: 4fjm
TitleRB69 DNA polymerase ternary complex with dCTP/dA
Components
  • DNA polymerase
  • DNA primerPrimer (molecular biology)
  • DNA template
KeywordsTransferase/DNA / dCTP/dA / RB69 / RB69pol / quadruple / 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, palm domain / Palm domain of DNA polymerase / B family DNA polymerase, finger domain / DNA polymerase, palm domain superfamily ...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, palm domain / Palm domain of DNA polymerase / B family DNA polymerase, finger domain / DNA polymerase, palm domain superfamily / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / Monooxygenase / DNA polymerase family B, exonuclease domain / DNA polymerase family B / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, exonuclease domain / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA (> 10) / DNA / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (bacteriophage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsXia, S. / Wang, J. / Konigsberg, W.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase.
Authors: Xia, S. / Wang, J. / Konigsberg, W.H.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA template
P: DNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3479
Polymers113,6803
Non-polymers6686
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-69 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)75.238, 119.744, 130.297
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: 104490.945 Da / Num. of mol.: 1 / Mutation: D222A, D327A, L561A, S565G, Y567A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (bacteriophage)
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 DNA template


Mass: 5237.399 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA primer / Primer (molecular biology)


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 472 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#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.: 466 / 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: 2.58 Å3/Da / Density % sol: 52.35 %

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 15, 2011
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 76737 / Num. obs: 72632 / % possible obs: 96 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 1.1
Reflection shellResolution: 2.02→2.09 Å / % possible all: 98.6

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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: 2.02→45.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.293 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23192 3853 5 %RANDOM
Rwork0.18767 ---
obs0.18989 72632 97.19 %-
all-76737 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.624 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å20 Å2
2--1.57 Å2-0 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.02→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7340 613 33 466 8452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198241
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.191.90511271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.724.182373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.469151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3941546
X-RAY DIFFRACTIONr_chiral_restr0.080.21164
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216089
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_it1.41444495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32667284
X-RAY DIFFRACTIONr_scbond_it2.82263742
X-RAY DIFFRACTIONr_scangle_it4.06593977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.065 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 231 -
Rwork0.261 4431 -
obs--84.17 %
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)
11.09540.00230.22030.1230.00320.0862-0.14860.0475-0.07310.02260.07110.0733-0.0285-0.0240.07750.0592-0.03380.01360.1397-0.0160.2382-17.5072.735.716
20.1796-0.11260.05651.1842-0.38840.2287-0-0.0235-0.0393-0.05-0.0218-0.08320.03960.0750.02190.03920.01310.00770.0590.00590.179424.914-2.30833.612
30.3439-0.2208-0.11660.75170.01711.09880.02650.0197-0.0413-0.0992-0.0555-0.0352-0.071-0.0940.02910.03380.00420.00450.0496-0.00570.124910.37921.83115.06
40.7603-0.46050.1340.89330.00370.3142-0.0796-0.2449-0.05720.13520.12350.03370.0014-0.0957-0.04380.0490.03010.01720.10750.02790.0924-3.726.58260.155
50.4654-0.2085-0.00462.43910.37330.3667-0.0822-0.07990.1095-0.06150.0414-0.0465-0.07890.05590.04080.0371-0.006-0.02630.0671-0.01180.13419.53626.34547.209
60.9178-0.21930.17460.5553-0.03351.1087-0.0892-0.04690.1466-0.01840.14250.0068-0.03810.0693-0.05330.04190.0238-0.02240.0833-0.0020.1487-9.46422.51547.668
71.51620.0072-0.34870.5030.45731.8838-0.07120.28510.0968-0.04370.10010.1002-0.0408-0.1602-0.0290.012-0.0275-0.02870.12010.05890.1399-22.30720.64627.886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T2 - 18
2X-RAY DIFFRACTION1P103 - 115
3X-RAY DIFFRACTION1A1001
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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