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- PDB-4xus: Crystal structure of the pre-catalytic ternary complex of DNA pol... -

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Basic information

Entry
Database: PDB / ID: 4xus
TitleCrystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming dTTP
Components
  • DNA (5'-D(*CP*AP*GP*TP*A)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / DNA POLYMERASE LAMBDA / PROTEIN-DNA COMPLEX / HELIX-HAIRPIN-HELIX / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBurak, M.J. / Guja, K.E. / Garcia-Diaz, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.
Authors: Burak, M.J. / Guja, K.E. / Garcia-Diaz, M.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references / Structure summary
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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
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.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 / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase lambda
D: DNA (5'-D(P*GP*CP*CP*G)-3')
P: DNA (5'-D(*CP*AP*GP*TP*A)-3')
T: DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3418
Polymers42,5194
Non-polymers8224
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-33 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 63.280, 141.060
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 lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 36448.594 Da / Num. of mol.: 1 / Fragment: UNP residues 251-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules DPT

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


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*GP*TP*A)-3')


Mass: 1504.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 259 molecules

#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DOC / 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 291.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O6P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate 2.0 M sodium formate
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→42 Å / Num. obs: 17565 / % possible obs: 86 % / Redundancy: 7.2 % / Biso Wilson estimate: 43.32 Å2 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.1 / % possible all: 44

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 2.4→41.96 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.8691 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.446 / SU Rfree Blow DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 896 5.1 %RANDOM
Rwork0.1874 ---
obs0.1898 17565 86.43 %-
Displacement parametersBiso mean: 29.24 Å2
Baniso -1Baniso -2Baniso -3
1--4.8485 Å20 Å20 Å2
2--6.3797 Å20 Å2
3----1.5311 Å2
Refine analyzeLuzzati coordinate error obs: 0.302 Å
Refinement stepCycle: LAST / Resolution: 2.4→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 406 49 255 5620
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015724HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9710307HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1199SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes882HARMONIC5
X-RAY DIFFRACTIONt_it5724HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion16.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion394SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5919SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.54 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.246 77 4.84 %
Rwork0.2022 1514 -
all0.2045 1591 -
obs--86.43 %
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)
11.2995-0.10980.45291.2410.44660.9880.01860.251-0.1173-0.11630.1017-0.1282-0.01690.1076-0.1203-0.1619-0.03310.0403-0.0378-0.0445-0.1314-13.897610.7447-15.2951
20.98140.34070.3885.49592.14881.9821-0.0340.0745-0.0188-0.0319-0.1003-0.1323-0.1209-0.05260.1342-0.396-0.01270.28350.11740.0186-0.1866-25.420514.8346-8.7894
33.7335-1.9509-1.53141.4884-0.54171.74750.01270.1169-0.0049-0.02790.0478-0.0797-0.1092-0.0115-0.06050.1635-0.0759-0.13020.13360.112-0.2325-20.14228.3461-29.844
42.3015-0.34141.38052.1799-1.20175.081-0.13530.4986-0.044-0.2968-0.14640.5114-0.1935-0.35060.2817-0.1230.03610.02180.11140.071-0.1144-27.119515.4803-17.3203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ P|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ T|* }

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