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- PDB-1bgx: TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB -

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Basic information

Entry
Database: PDB / ID: 1bgx
TitleTAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB
Components
  • (TP7 MAB) x 2
  • TAQ DNA POLYMERASE
KeywordsCOMPLEX (POLYMERASE/INHIBITOR) / DNA POLYMERASE / FAB / PCR / INHIBITION / HELIX-COIL DYNAMICS / INHIBITOR DESIGN / COMPLEX (POLYMERASE-INHIBITOR) / COMPLEX (POLYMERASE-INHIBITOR) 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 / 5'-nuclease / 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 polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / 5'-nuclease / 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 / Immunoglobulins / DNA/RNA polymerase superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / : / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMurali, R. / Sharkey, D.J. / Daiss, J.L. / Krishna Murthy, H.M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme.
Authors: Murali, R. / Sharkey, D.J. / Daiss, J.L. / Murthy, H.M.
#1: Journal: Protein Eng. / Year: 1998
Title: Structural Studies on an Inhibitory Antibody Against Thermus Aquaticus DNA Polymerase Suggest Mode of Inhibition
Authors: Murali, R. / Helmer-Citterich, M. / Sharkey, D.J. / Scalice, E.R. / Daiss, J.L. / Sullivan, M.A. / Krishna Murthy, H.M.
History
DepositionJun 2, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: TAQ DNA POLYMERASE
L: TP7 MAB
H: TP7 MAB


Theoretical massNumber of molelcules
Total (without water)140,7193
Polymers140,7193
Non-polymers00
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-42 kcal/mol
Surface area53510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 89.100, 89.300
Angle α, β, γ (deg.)100.70, 115.30, 95.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TAQ DNA POLYMERASE


Mass: 94046.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: TAQ / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase
#2: Antibody TP7 MAB


Mass: 23082.521 Da / Num. of mol.: 1 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA / Production host: Mus musculus (house mouse) / References: GenBank: 437099
#3: Antibody TP7 MAB


Mass: 23590.266 Da / Num. of mol.: 1 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA / Production host: Mus musculus (house mouse) / References: GenBank: 1513182
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PROTEIN WAS CRYSTALLIZED FROM 22% PEG 3350, 200 MM TRIS/HCL, PH 7.4. COMPLEX WAS MADE AT A PROTEIN CONCENTRATION OF 0.5 MG/ML, LEFT FOR 2-3 DAYS AT 4 DEGREES CELSIUS, CONCENTRATED TO 5MG/ML ...Details: PROTEIN WAS CRYSTALLIZED FROM 22% PEG 3350, 200 MM TRIS/HCL, PH 7.4. COMPLEX WAS MADE AT A PROTEIN CONCENTRATION OF 0.5 MG/ML, LEFT FOR 2-3 DAYS AT 4 DEGREES CELSIUS, CONCENTRATED TO 5MG/ML PROTEIN AND CRYSTALLIZATION CARRIED OUT IN HANGING DROPS., vapor diffusion - hanging drop, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
222 %PEG33501reservoir
3200 mMTris-HCl1reservoirpH7.4
40.1 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→27.7 Å / Num. obs: 81111 / % possible obs: 82 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.2
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 8 / % possible all: 75.9
Reflection
*PLUS
Num. measured all: 414722

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYL AND 1TAQ

1ayl

1taq


Resolution: 2.3→8 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 100000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4080 5 %RANDOM
Rwork0.189 ---
obs0.189 81111 82 %-
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9814 0 0 263 10077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.41.5
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scbond_it2.42
X-RAY DIFFRACTIONx_scangle_it2.82.5
LS refinement shellResolution: 2.3→2.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 680 5 %
Rwork0.25 13519 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rwork: 0.25

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