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- PDB-1t94: Crystal structure of the catalytic core of human DNA polymerase kappa -

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Basic information

Entry
Database: PDB / ID: 1t94
TitleCrystal structure of the catalytic core of human DNA polymerase kappa
Componentspolymerase (DNA directed) kappa
KeywordsREPLICATION / DNA repair / Y-family DNA polymerase / Translesion DNA synthesis / Lesion bypass
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV ...nucleotide-excision repair, DNA gap filling / error-prone translesion synthesis / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I ...DNA polymerase; domain 1 - #810 / Rad18-like CCHC zinc finger / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase kappa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsUljon, S.N. / Johnson, R.E. / Edwards, T.A. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structure of the catalytic core of human DNA polymerase kappa.
Authors: Uljon, S.N. / Johnson, R.E. / Edwards, T.A. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
History
DepositionMay 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polymerase (DNA directed) kappa
B: polymerase (DNA directed) kappa


Theoretical massNumber of molelcules
Total (without water)104,8062
Polymers104,8062
Non-polymers00
Water6,485360
1
A: polymerase (DNA directed) kappa


Theoretical massNumber of molelcules
Total (without water)52,4031
Polymers52,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: polymerase (DNA directed) kappa


Theoretical massNumber of molelcules
Total (without water)52,4031
Polymers52,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.209, 109.460, 111.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein polymerase (DNA directed) kappa / DINB protein / polymerase (DNA-directed) kappa


Mass: 52402.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DINB / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon + / References: UniProt: Q9UBT6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.485 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 8% PEG 8K, 8% Ethylene Glycol, and 100mM HEPES (pH 7.75), VAPOR DIFFUSION, HANGING DROP, temperature 20K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B11.12709
SYNCHROTRONAPS 19-ID20.97934, 0.97920, 0.96859
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJun 13, 2003Diamond (111) double-crystal monochromator
SBC-22CCDJun 30, 2003Bent cylindrical Si-mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2si 111 / si 220MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.127091
20.979341
30.97921
40.968591
ReflectionResolution: 2.4→50 Å / Num. obs: 76925 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.019 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→20.03 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3842947.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 3529 4.9 %RANDOM
Rwork0.246 ---
obs0.246 71651 91.2 %-
all-78579 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8708 Å2 / ksol: 0.33302 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--8.97 Å20 Å20 Å2
2--5.15 Å20 Å2
3---3.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→20.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6172 0 0 360 6532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 501 4.7 %
Rwork0.33 10070 -
obs--80.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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