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- PDB-5ddy: Binary complex of human Polymerase lambda with dCTP -

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Basic information

Entry
Database: PDB / ID: 5ddy
TitleBinary complex of human Polymerase lambda with dCTP
ComponentsDNA polymerase lambda
KeywordsTRANSFERASE / Polymerase lambda
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 / double-strand break repair via homologous recombination / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / 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 / double-strand break repair via homologous recombination / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / 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'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / : / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
AuthorsLiu, M.S. / Tsai, M.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda
Authors: Liu, M.S. / Tsai, H.Y. / Liu, X.X. / Ho, M.C. / Wu, W.J. / Tsai, M.D.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: 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
A: DNA polymerase lambda
C: DNA polymerase lambda
E: DNA polymerase lambda
G: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,32420
Polymers149,9194
Non-polymers2,40516
Water543
1
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0815
Polymers37,4801
Non-polymers6014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0815
Polymers37,4801
Non-polymers6014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0815
Polymers37,4801
Non-polymers6014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0815
Polymers37,4801
Non-polymers6014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.015, 206.015, 114.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 37479.750 Da / Num. of mol.: 4 / Fragment: UNP residues 242-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGP5, DNA-directed DNA polymerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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

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Sample preparation

CrystalDensity Matthews: 4.04 Å3/Da / Density % sol: 69.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 3.0M Sodium Chloride

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.36→30 Å / Num. obs: 35439 / % possible obs: 99.8 % / Redundancy: 11 % / Biso Wilson estimate: 119.31 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1 / Net I/av σ(I): 26.277 / Net I/σ(I): 16.3 / Num. measured all: 390025
Reflection shell

Χ2: 1 / Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique all% possible all
3.37-3.499.80.825343899.1
3.49-3.6310.50.614348799.8
3.63-3.7910.90.392349199.9
3.79-3.9911.20.2633515100
3.99-4.2411.50.1493506100
4.24-4.5711.70.113530100
4.57-5.0311.70.0833545100
5.03-5.7511.60.0713561100
5.75-7.2311.10.0593609100
7.23-30100.034375799

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XSL

1xsl


Resolution: 3.36→29.658 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2969 1832 5.68 %
Rwork0.2618 --
obs0.2637 32255 90.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.36→29.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8949 0 124 3 9076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029254
X-RAY DIFFRACTIONf_angle_d0.6312517
X-RAY DIFFRACTIONf_dihedral_angle_d13.8443475
X-RAY DIFFRACTIONf_chiral_restr0.0241356
X-RAY DIFFRACTIONf_plane_restr0.0031616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3599-3.45060.44551280.3872038X-RAY DIFFRACTION81
3.4506-3.5520.42711310.36882118X-RAY DIFFRACTION84
3.552-3.66640.36531300.3592188X-RAY DIFFRACTION86
3.6664-3.79720.36091260.31382214X-RAY DIFFRACTION88
3.7972-3.94890.34991350.31892203X-RAY DIFFRACTION87
3.9489-4.12820.36071340.28832303X-RAY DIFFRACTION90
4.1282-4.34520.2921350.27412352X-RAY DIFFRACTION92
4.3452-4.61650.32261450.25862385X-RAY DIFFRACTION94
4.6165-4.97140.29061490.24482440X-RAY DIFFRACTION95
4.9714-5.46890.24711510.24772476X-RAY DIFFRACTION96
5.4689-6.25380.27821550.27362511X-RAY DIFFRACTION97
6.2538-7.85480.30841540.26042581X-RAY DIFFRACTION98
7.8548-29.65950.23651590.20842614X-RAY DIFFRACTION95

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