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- PDB-4bwm: KlenTaq mutant in complex with a RNA/DNA hybrid -

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Basic information

Entry
Database: PDB / ID: 4bwm
TitleKlenTaq mutant in complex with a RNA/DNA hybrid
Components
  • 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOCP)-3'
  • 5'-R(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*UP*GP*GP*UP*C)-3'
  • DNA POLYMERASE I, THERMOSTABLE
KeywordsTRANSFERASE/DNA/RNA / TRANSFERASE-DNA-RNA COMPLEX
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / 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 / DNA polymerase 1 / 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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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 / FORMIC ACID / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 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 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection / Database references / Source and taxonomy
Revision 1.3May 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 1.4Dec 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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'
G: 5'-R(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*UP*GP*GP*UP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,64613
Polymers69,8673
Non-polymers77910
Water11,367631
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-66.1 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.192, 86.282, 63.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / DNA chain / RNA chain , 3 types, 3 molecules ABG

#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
#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: RNA chain 5'-R(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*UP*GP*GP*UP*C)-3' / TEMPLATE


Mass: 5192.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 641 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 3.21 Å3/Da / Density % sol: 61.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP. 100MM TRIS PH8.5, 200MM MG-FORMATE, 20% PEG 8K MICROSEEDED

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 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: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.75→47.34 Å / Num. obs: 79729 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.59 % / Biso Wilson estimate: 26.55 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.73
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 6.62 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1411)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RTV

3rtv


Resolution: 1.749→47.985 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 19.98 / Stereochemistry target values: ML
Details: RESIDUES 15 AND 16 OF THE TEMPLATE AND 1 AND 2 OF THE PRIMER ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2076 3989 5 %
Rwork0.168 --
obs0.17 79632 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.749→47.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 504 44 631 5467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075043
X-RAY DIFFRACTIONf_angle_d1.0896942
X-RAY DIFFRACTIONf_dihedral_angle_d14.6981992
X-RAY DIFFRACTIONf_chiral_restr0.07767
X-RAY DIFFRACTIONf_plane_restr0.005819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7488-1.77010.28441260.25742580X-RAY DIFFRACTION97
1.7701-1.79250.25631240.24812701X-RAY DIFFRACTION100
1.7925-1.81610.27151490.24292673X-RAY DIFFRACTION100
1.8161-1.8410.25171370.23162682X-RAY DIFFRACTION100
1.841-1.86730.23231470.22552645X-RAY DIFFRACTION100
1.8673-1.89520.22171410.21532659X-RAY DIFFRACTION100
1.8952-1.92480.24721440.20932693X-RAY DIFFRACTION100
1.9248-1.95640.24651420.19632674X-RAY DIFFRACTION100
1.9564-1.99010.2191340.19442673X-RAY DIFFRACTION100
1.9901-2.02630.23171620.19442658X-RAY DIFFRACTION100
2.0263-2.06530.2121440.17992684X-RAY DIFFRACTION100
2.0653-2.10740.19281350.17772687X-RAY DIFFRACTION100
2.1074-2.15320.20651370.16712676X-RAY DIFFRACTION100
2.1532-2.20330.19531450.16292687X-RAY DIFFRACTION100
2.2033-2.25840.19021390.16172702X-RAY DIFFRACTION100
2.2584-2.31950.23311310.17172697X-RAY DIFFRACTION100
2.3195-2.38770.1991470.17162691X-RAY DIFFRACTION100
2.3877-2.46480.23821490.16972683X-RAY DIFFRACTION100
2.4648-2.55290.22141320.17432717X-RAY DIFFRACTION100
2.5529-2.65510.22531520.18062675X-RAY DIFFRACTION100
2.6551-2.77590.21911620.18272704X-RAY DIFFRACTION100
2.7759-2.92230.24581160.17942724X-RAY DIFFRACTION100
2.9223-3.10530.23381400.17932724X-RAY DIFFRACTION100
3.1053-3.3450.22551360.17222764X-RAY DIFFRACTION100
3.345-3.68150.19221670.14952710X-RAY DIFFRACTION100
3.6815-4.2140.171530.13362758X-RAY DIFFRACTION100
4.214-5.30810.16161460.13682791X-RAY DIFFRACTION100
5.3081-48.0030.21481520.16252931X-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)
10.6949-0.11490.29410.17030.08340.2182-0.1084-0.03910.20610.02460.0293-0.0949-0.03450.0033-00.095-0.0075-0.02330.0929-0.00450.191-9.156919.18252.6349
20.0607-0.0310.11730.05590.08570.32270.0375-0.02650.0176-0.0829-0.0246-0.04720.0744-0.013300.1672-0.0037-0.01540.10110.00310.0803-22.4906-10.5362-11.5175
30.1809-0.0230.22350.4115-0.48340.78270.0355-0.04910.0509-0.09870.11620.11010.0867-0.083700.12340.0099-0.04460.13150.05030.1068-40.25417.9901-11.8373
40.152-0.03550.04860.08030.04110.13370.0146-0.0535-0.04610.04740.02830.08810.0226-0.0845-00.08890.01390.00690.13810.02610.1055-33.0566-0.15138.8692
5-0.0060.0170.02660.01650.00630.06980.0520.03990.46980.06590.19240.00560.4443-0.037500.258-0.0434-0.00180.18960.01330.1345-19.71430.9984-22.9811
6-0.0659-0.05330.0036-0.08160.04070.0791-0.28690.27630.21770.13650.1423-0.0839-0.00420.119100.1179-0.01590.00320.32390.01280.145-22.67652.438-23.8398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 295 THROUGH 433 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 434 THROUGH 603 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 604 THROUGH 775 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 776 THROUGH 832 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 103 THROUGH 111 )
6X-RAY DIFFRACTION6CHAIN G AND (RESID 1 THROUGH 14 )

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