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- PDB-4bwj: KlenTaq mutant in complex with DNA and ddCTP -

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Basic information

Entry
Database: PDB / ID: 4bwj
TitleKlenTaq mutant in complex with DNA and ddCTP
Components
  • 5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP)-3'
  • 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3'
  • DNA POLYMERASE I, THERMOSTABLE
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSFERASE
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBlatter, N. / Bergen, K. / Welte, W. / Diederichs, K. / Marx, A.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Structure and Function of an RNA-Reading Thermostable DNA Polymerase.
Authors: Blatter, N. / Bergen, K. / Nolte, O. / Welte, W. / Diederichs, K. / Mayer, J. / Wieland, M. / Marx, A.
#1: Journal: Angew.Chem. / Year: 2013
Title: Struktur Und Funktion Einer RNA-Lesenden Thermostabilen DNA-Polymerase
Authors: Blatter, N. / Bergen, K. / Nolte, O. / Welte, W. / Diederichs, K. / Mayer, J. / Wieland, M. / Marx, A.
History
DepositionJul 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Atomic model
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Sep 23, 2015Group: Data collection / Database references / Source and taxonomy
Revision 1.5May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_conn_type.id / _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 I, THERMOSTABLE
B: 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3'
C: 5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2119
Polymers69,6393
Non-polymers5736
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-42.9 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.143, 108.143, 89.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2277-

HOH

21A-2278-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA POLYMERASE I, THERMOSTABLE / TAQ POLYMERASE 1


Mass: 61057.113 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT, RESIDUES 293-832 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Plasmid: PGDR11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3' / PRIMER


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*CP)-3' / TEMPLATE


Mass: 4964.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 487 molecules

#4: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINALLY TRUNCATED, KLENOW FRAGMENT

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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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP. 100MM TRIS PH 7.5, 200MM MG-FORMATE, 15% PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→46.83 Å / Num. obs: 88092 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8.57 % / Biso Wilson estimate: 29.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.56
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 8.62 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.64 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RTV

3rtv


Resolution: 1.55→46.827 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 4377 5 %
Rwork0.1583 --
obs0.1605 87950 99.95 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→46.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 531 32 481 5332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115082
X-RAY DIFFRACTIONf_angle_d1.5047004
X-RAY DIFFRACTIONf_dihedral_angle_d15.9351988
X-RAY DIFFRACTIONf_chiral_restr0.078762
X-RAY DIFFRACTIONf_plane_restr0.008824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.56770.29981360.30262705X-RAY DIFFRACTION99
1.5677-1.58610.32881570.27842764X-RAY DIFFRACTION100
1.5861-1.60550.28311260.26282763X-RAY DIFFRACTION100
1.6055-1.62580.27761340.24442784X-RAY DIFFRACTION100
1.6258-1.64720.25631360.23362754X-RAY DIFFRACTION100
1.6472-1.66970.26461300.22122769X-RAY DIFFRACTION100
1.6697-1.69360.23031500.21842802X-RAY DIFFRACTION100
1.6936-1.71890.26171360.20652774X-RAY DIFFRACTION100
1.7189-1.74570.26381470.21052769X-RAY DIFFRACTION100
1.7457-1.77440.23791480.19942762X-RAY DIFFRACTION100
1.7744-1.8050.23971460.19572752X-RAY DIFFRACTION100
1.805-1.83780.25111590.18892759X-RAY DIFFRACTION100
1.8378-1.87310.20621480.18072791X-RAY DIFFRACTION100
1.8731-1.91140.22171510.17672730X-RAY DIFFRACTION100
1.9114-1.95290.24871470.18362779X-RAY DIFFRACTION100
1.9529-1.99840.22271630.18082767X-RAY DIFFRACTION100
1.9984-2.04830.21911530.17912731X-RAY DIFFRACTION100
2.0483-2.10370.24891360.17372799X-RAY DIFFRACTION100
2.1037-2.16560.20281300.16432822X-RAY DIFFRACTION100
2.1656-2.23550.21741280.16692805X-RAY DIFFRACTION100
2.2355-2.31540.21321450.15822763X-RAY DIFFRACTION100
2.3154-2.40810.2221300.1582809X-RAY DIFFRACTION100
2.4081-2.51770.20831590.162771X-RAY DIFFRACTION100
2.5177-2.65040.23361480.16252805X-RAY DIFFRACTION100
2.6504-2.81650.20491500.16962790X-RAY DIFFRACTION100
2.8165-3.03390.21561490.172798X-RAY DIFFRACTION100
3.0339-3.33910.19141480.1562832X-RAY DIFFRACTION100
3.3391-3.82210.16251650.13542816X-RAY DIFFRACTION100
3.8221-4.81470.15231580.12062847X-RAY DIFFRACTION100
4.8147-46.84870.2121640.15182961X-RAY DIFFRACTION100
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)
10.68080.1865-0.02681.33770.30180.79720.0021-0.0222-0.0259-0.01070.0083-0.03970.04350.0061-0.00870.1373-0.0188-0.0130.19110.03440.167837.4832-26.0212-8.3595
21.50730.7104-0.3241.8963-1.41273.3947-0.0019-0.09050.25880.24320.24290.4077-0.4747-0.7609-0.230.26970.0729-0.00180.38590.0260.278315.3054-20.7972-11.4213
38.6586-3.04552.81383.3288-1.40831.89140.06830.2363-0.42330.1538-0.126-0.13410.04090.34220.04620.2364-0.03030.01160.2690.00170.262737.4865-23.25575.1043
44.13430.05352.13041.86530.35172.2125-0.2223-0.2808-0.08490.16550.1887-0.108-0.0482-0.09280.03420.24230.00910.02620.2770.01280.202235.6711-23.67515.1377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 294:603)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 604:832)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 101:111)
4X-RAY DIFFRACTION4CHAIN C AND (RESSEQ 204:216)

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