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- PDB-4i9q: Crystal structure of the ternary complex of the D714A mutant of R... -

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Basic information

Entry
Database: PDB / ID: 4i9q
TitleCrystal structure of the ternary complex of the D714A mutant of RB69 DNA polymerase
Components
  • DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')
  • DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / PALM SUBDOMAIN / HYDROLASE / 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
Chem-XG4 / DNA / DNA (> 10) / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGuja, K.E. / Jacewicz, A. / Trzemecka, A. / Plochocka, D. / Yakubovskaya, E. / Bebenek, A. / Garcia-Diaz, M.
CitationJournal: Plos One / Year: 2013
Title: A Remote Palm Domain Residue of RB69 DNA Polymerase Is Critical for Enzyme Activity and Influences the Conformation of the Active Site.
Authors: Jacewicz, A. / Trzemecka, A. / Guja, K.E. / Plochocka, D. / Yakubovskaya, E. / Bebenek, A. / Garcia-Diaz, M.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_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.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_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(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
B: DNA polymerase
P: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')
D: DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
C: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,12714
Polymers227,9766
Non-polymers2,1518
Water7,170398
1
A: DNA polymerase
T: DNA (5'-D(*TP*CP*AP*CP*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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0647
Polymers113,9883
Non-polymers1,0754
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-36 kcal/mol
Surface area39530 Å2
MethodPISA
2
B: DNA polymerase
D: DNA (5'-D(*TP*CP*AP*CP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')
C: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0647
Polymers113,9883
Non-polymers1,0754
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-40 kcal/mol
Surface area42050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.781, 119.412, 146.016
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase / / Gp43


Mass: 104519.039 Da / Num. of mol.: 2 / Mutation: D222A D327A,Y567A,D714A
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, 4 molecules TDPC

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


Mass: 5501.567 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3')


Mass: 3967.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 4 types, 406 molecules

#4: Chemical
ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 8000, 0.2 M (NH4)2SO4 and 0.1 M sodium citrate (pH 5.6), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.117 Å / Num. obs: 110655

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1227)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGI

3ngi


Resolution: 2.3→38.403 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 5526 5 %
Rwork0.2519 --
obs0.2537 110586 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13979 1234 128 398 15739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01216073
X-RAY DIFFRACTIONf_angle_d0.78122068
X-RAY DIFFRACTIONf_dihedral_angle_d15.6886179
X-RAY DIFFRACTIONf_chiral_restr0.0512337
X-RAY DIFFRACTIONf_plane_restr0.0032618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.29351930.26643466X-RAY DIFFRACTION100
2.3261-2.35350.36851990.26853527X-RAY DIFFRACTION100
2.3535-2.38220.34422050.27033566X-RAY DIFFRACTION100
2.3822-2.41230.33121810.27833486X-RAY DIFFRACTION100
2.4123-2.44410.34631850.27043539X-RAY DIFFRACTION100
2.4441-2.47760.31271950.26943527X-RAY DIFFRACTION100
2.4776-2.51290.3381920.26123508X-RAY DIFFRACTION100
2.5129-2.55040.31652090.26493560X-RAY DIFFRACTION100
2.5504-2.59030.31051720.26083506X-RAY DIFFRACTION100
2.5903-2.63270.3091570.26593588X-RAY DIFFRACTION100
2.6327-2.67810.29341750.27043484X-RAY DIFFRACTION100
2.6781-2.72680.33591780.27053587X-RAY DIFFRACTION100
2.7268-2.77930.3321860.27313500X-RAY DIFFRACTION100
2.7793-2.8360.32931660.27143576X-RAY DIFFRACTION100
2.836-2.89760.30941790.27543508X-RAY DIFFRACTION100
2.8976-2.9650.33592040.27593514X-RAY DIFFRACTION99
2.965-3.03910.31671750.27683517X-RAY DIFFRACTION99
3.0391-3.12120.33761730.27443529X-RAY DIFFRACTION99
3.1212-3.2130.3341920.27473525X-RAY DIFFRACTION99
3.213-3.31670.28911750.27143444X-RAY DIFFRACTION97
3.3167-3.43520.31061640.26053428X-RAY DIFFRACTION96
3.4352-3.57260.29431850.26133460X-RAY DIFFRACTION97
3.5726-3.73510.30931870.26213443X-RAY DIFFRACTION97
3.7351-3.93180.26291910.24473409X-RAY DIFFRACTION96
3.9318-4.17790.23831650.23523444X-RAY DIFFRACTION96
4.1779-4.50.24941820.23463439X-RAY DIFFRACTION96
4.5-4.9520.25551710.2233492X-RAY DIFFRACTION97
4.952-5.66660.27242020.22653473X-RAY DIFFRACTION97
5.6666-7.13190.25271980.24463463X-RAY DIFFRACTION97
7.1319-38.4080.22611900.21563552X-RAY DIFFRACTION97
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)
11.287-2.6781-0.05617.209-0.22140.90240.16050.2382-0.0191-0.8963-0.2120.30890.06050.02440.05180.3140.0009-0.04470.24730.0090.2278-7.03771.8808-26.9698
23.3531-1.02520.05071.9749-0.19471.03810.09070.03370.1497-0.2239-0.0803-0.2188-0.21720.0124-0.01310.2782-0.01370.03230.2119-0.03640.159212.8602-20.7525-16.1512
30.70340.3689-0.65230.8265-1.31133.304-0.0017-0.11350.0352-0.2499-0.06160.06310.20880.12010.05850.1262-0.007-0.02370.2809-0.02370.316-18.5609-1.9547-0.928
41.7187-0.43850.47260.89-0.28950.8166-0.0039-0.0368-0.12320.03880.01740.06480.0474-0.0425-0.01240.1575-0.01510.00910.1811-0.05840.1482-4.8249-16.737816.9877
54.4505-0.29672.2051.8554-1.86142.70470.04930.070.21860.1765-0.0751-0.207-0.21450.49510.03070.2026-0.0146-0.03670.2265-0.03150.33424.65160.063713.9551
61.3811.54550.14152.5528-0.15080.35980.1207-0.18720.03840.5307-0.1536-0.02050.0043-0.0440.03230.58110.01080.04350.2606-0.01370.239-36.8982-1.8078-48.4716
71.40381.0708-0.05171.48250.37180.7460.13720.03620.3807-0.0316-0.06810.1149-0.9269-0.1627-0.04010.73890.060.02890.26260.02640.3462-44.7704-2.9874-57.5774
80.5123-0.0118-0.15510.35570.05450.3777-0.0038-0.0236-0.08470.1108-0.0616-0.18180.0594-0.0050.06430.48020.0382-0.03460.2311-0.0030.2962-23.7882-2.6002-70.9816
90.96780.31560.06780.72290.18240.16860.04260.1183-0.1263-0.00070.0132-0.03670.08680.0206-0.05350.39510.0605-0.05490.23280.01020.2011-33.9277-6.7969-89.72
103.7671.43910.53693.00881.09281.7923-0.0344-0.45110.06520.52970.244-0.4611-0.1809-0.1162-0.20380.33830.0693-0.09650.32520.00820.3724.5314-1.799519.1095
112.71350.75233.24253.34041.19294.35240.248-0.0097-0.0880.62980.28790.35490.3044-0.9011-0.52170.41420.1477-0.02120.51630.06680.3565-35.69066.1625-79.0156
122.53090.4771-1.70210.35410.29532.5774-0.08130.57820.6972-0.51190.20820.4517-0.6619-0.4986-0.12530.6730.1506-0.25670.48060.11240.6657-53.68119.8929-96.6687
134.34770.74853.25781.4962-0.39997.99420.20370.8061-0.4346-0.76110.0792-0.0241-0.03880.3429-0.27120.91070.0587-0.25870.7142-0.0580.5821-48.819110.9585-98.1066
140.917-0.4594-0.00050.58890.08040.5524-0.08730.28280.08450.0483-0.05790.0336-0.1731-0.08680.14410.37110.1383-0.07520.3951-0.04270.2682-38.58161.4536-83.3249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 360 )
3X-RAY DIFFRACTION3chain 'A' and (resid 361 through 579 )
4X-RAY DIFFRACTION4chain 'A' and (resid 580 through 895 )
5X-RAY DIFFRACTION5chain 'T' and (resid 1 through 18 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 207 )
7X-RAY DIFFRACTION7chain 'B' and (resid 208 through 298 )
8X-RAY DIFFRACTION8chain 'B' and (resid 299 through 557 )
9X-RAY DIFFRACTION9chain 'B' and (resid 558 through 900 )
10X-RAY DIFFRACTION10chain 'P' and (resid 103 through 115 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 10 )
12X-RAY DIFFRACTION12chain 'D' and (resid 11 through 17 )
13X-RAY DIFFRACTION13chain 'C' and (resid 103 through 109 )
14X-RAY DIFFRACTION14chain 'C' and (resid 110 through 115 )

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