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- PDB-4khq: Ternary complex of RB69 mutant L415F wit DUMPNPP -

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Basic information

Entry
Database: PDB / ID: 4khq
TitleTernary complex of RB69 mutant L415F wit DUMPNPP
Components
  • DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / NUCLEOTIDE / 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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.186 Å
AuthorsClausen, A.R. / Pedersen, L.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure-function analysis of ribonucleotide bypass by B family DNA replicases.
Authors: Clausen, A.R. / Murray, M.S. / Passer, A.R. / Pedersen, L.C. / Kunkel, T.A.
History
DepositionMay 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Feb 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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_id / _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: DNA (5'-D(*AP*CP*AP*GP*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*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,26815
Polymers114,4973
Non-polymers77112
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-123 kcal/mol
Surface area42000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.659, 119.360, 128.070
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: 104689.156 Da / Num. of mol.: 1 / Mutation: D327A, D222A, L415F
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 DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')


Mass: 5550.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE STRAND
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*C)-3')


Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PRIMER STRAND

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Non-polymers , 4 types, 590 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 MM TRIS, PH 7.5, 10% PEG350, 180 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2010
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.186→50 Å / Num. all: 64251 / Num. obs: 64251 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.074 / Net I/σ(I): 11.9
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.52 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)model building
PHENIX(PHENIX.REFINE: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.186→46.236 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 3204 4.99 %
Rwork0.1791 --
obs0.1808 64171 99.22 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.271 Å2-0 Å20 Å2
2---3.3492 Å20 Å2
3---5.2892 Å2
Refinement stepCycle: LAST / Resolution: 2.186→46.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 649 39 578 8481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018339
X-RAY DIFFRACTIONf_angle_d0.72411485
X-RAY DIFFRACTIONf_dihedral_angle_d11.5172805
X-RAY DIFFRACTIONf_chiral_restr0.0511213
X-RAY DIFFRACTIONf_plane_restr0.0031374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1857-2.21830.2641050.23442215X-RAY DIFFRACTION84
2.2183-2.25290.28921470.22792610X-RAY DIFFRACTION99
2.2529-2.28990.29281370.23252645X-RAY DIFFRACTION100
2.2899-2.32940.26531430.21922613X-RAY DIFFRACTION100
2.3294-2.37170.28561480.21442653X-RAY DIFFRACTION100
2.3717-2.41730.23271200.20342627X-RAY DIFFRACTION100
2.4173-2.46670.27111390.20642655X-RAY DIFFRACTION100
2.4667-2.52030.25891490.20222643X-RAY DIFFRACTION100
2.5203-2.57890.2321280.20872652X-RAY DIFFRACTION100
2.5789-2.64340.26861730.2072615X-RAY DIFFRACTION100
2.6434-2.71490.25781450.20762666X-RAY DIFFRACTION100
2.7149-2.79480.27571400.20722631X-RAY DIFFRACTION100
2.7948-2.8850.22241320.20262656X-RAY DIFFRACTION100
2.885-2.9880.21861360.21162675X-RAY DIFFRACTION100
2.988-3.10770.25371300.1982669X-RAY DIFFRACTION100
3.1077-3.24910.27981290.20422674X-RAY DIFFRACTION100
3.2491-3.42030.21381420.18942668X-RAY DIFFRACTION100
3.4203-3.63450.21360.1772690X-RAY DIFFRACTION100
3.6345-3.9150.19881480.16322677X-RAY DIFFRACTION100
3.915-4.30870.15171470.13952690X-RAY DIFFRACTION100
4.3087-4.93160.15671430.12742723X-RAY DIFFRACTION100
4.9316-6.21090.17011600.15852745X-RAY DIFFRACTION100
6.2109-46.24660.21311270.17772875X-RAY DIFFRACTION99
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)
10.63611.00080.04674.39-1.65432.17990.0772-0.03560.09970.1991-0.2239-0.5474-0.14280.18540.16320.2207-0.00320.02290.35590.05720.546828.888563.098233.7896
20.72640.4215-0.45082.7685-0.36151.9139-0.0193-0.0941-0.08360.3722-0.1945-0.11460.2081-0.15170.20820.3073-0.0157-0.07850.33160.0140.308212.509530.604152.8885
31.71691.8152-0.43113.12430.53974.89870.1648-0.27550.25180.436-0.1771-0.1833-0.37870.02850.02150.3183-0.0047-0.08760.29440.00020.321415.897546.449753.4396
42.1476-0.71510.80791.58840.78692.95640.0173-0.0932-0.08940.07730.06590.32760.2193-0.4541-0.08110.25510.00770.01640.28530.03630.27440.232535.335139.6682
50.58470.1720.06431.266-0.2750.70440.03740.00420.0853-0.1148-0.0895-0.12070.13380.00210.04470.22540.02730.02490.2375-0.00930.23637.600446.137329.0318
61.3590.26250.29162.9209-0.48941.5712-0.01660.2184-0.1248-0.40780.0194-0.22920.47980.1398-0.00590.45920.08420.12050.3663-0.01110.21478.656142.649411.2772
71.27210.04890.03871.7242-0.40510.8863-0.05550.3861-0.0208-0.680.05180.11220.4225-0.02920.00040.5484-0.0095-0.00020.34650.020.2196-0.872346.44046.5351
81.5716-1.1284-0.4351.92040.2011.8286-0.00870.1979-0.1655-0.3146-0.00920.11630.55370.05030.0290.6436-0.0221-0.05070.32440.00660.308-10.418734.774311.1918
91.9528-0.0994-0.15512.1520.73313.5165-0.0474-0.3697-0.08620.12150.03140.29250.1618-0.17010.01910.2503-0.00410.00080.31750.07520.3463-20.020738.430339.1905
103.17691.26380.55312.43140.62651.8367-0.20490.156-0.0821-0.4773-0.25760.3428-0.0911-0.39830.46150.407-0.0479-0.09520.49940.02290.5483-32.372334.910220.2484
112.38040.65691.47163.72530.79592.8013-0.06530.2944-0.2684-0.2539-0.12380.39910.83940.07280.10170.44230.08380.09250.77920.18611.0132-35.534458.003130.0529
126.567-2.52243.17333.657-0.57673.5451-0.3321.03881.70480.26360.1068-0.0138-0.6990.02630.15290.3273-0.0221-0.02780.50760.14160.9172-19.76360.182832.418
131.00340.4131-0.16930.7904-0.94771.9604-0.12710.13490.1376-0.14410.0679-0.01730.2442-0.3690.06220.2908-0.0190.00320.34250.03020.3263-9.081348.502626.6218
146.4105-0.81640.95962.9587-1.54381.1712-0.0948-0.66740.54280.14680.0097-0.0466-0.0577-0.04010.10860.22710.05790.06630.2927-0.01190.2796-3.050956.998426.1791
156.4547-1.7432-4.39645.84652.1423.229-0.55670.4080.36280.58440.21250.44950.5007-1.21960.29480.35730.00950.05230.45930.06690.5303-23.022951.570832.047
164.95040.46092.60631.3783-0.091.4881-1.29350.05341.4040.5490.251-0.49090.01420.59890.9990.46010.1865-0.01240.60480.06090.8598-37.246164.4332.796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:99)
2X-RAY DIFFRACTION2(chain A and resid 100:197)
3X-RAY DIFFRACTION3(chain A and resid 198:270)
4X-RAY DIFFRACTION4(chain A and resid 271:310)
5X-RAY DIFFRACTION5(chain A and resid 311:416)
6X-RAY DIFFRACTION6(chain A and resid 417:541)
7X-RAY DIFFRACTION7(chain A and resid 542:683)
8X-RAY DIFFRACTION8(chain A and resid 684:724)
9X-RAY DIFFRACTION9(chain A and resid 725:870)
10X-RAY DIFFRACTION10(chain A and resid 871:902)
11X-RAY DIFFRACTION11(chain P and resid 102:106)
12X-RAY DIFFRACTION12(chain P and resid 107:110)
13X-RAY DIFFRACTION13(chain P and resid 111:115)
14X-RAY DIFFRACTION14(chain T and resid 1:8)
15X-RAY DIFFRACTION15(chain T and resid 9:12)
16X-RAY DIFFRACTION16(chain T and resid 13:18)

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