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- PDB-1jih: Yeast DNA Polymerase ETA -

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Basic information

Entry
Database: PDB / ID: 1jih
TitleYeast DNA Polymerase ETA
ComponentsDNA Polymerase ETA
KeywordsTRANSLATION / DNA Polymerase / translesion / yeast
Function / homology
Function and homology information


mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase ...mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / metal ion binding / nucleus
Similarity search - Function
DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain ...DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / 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 / 5' to 3' exonuclease, C-terminal subdomain / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsTrincao, J. / Johnson, R.E. / Escalante, C.R. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
CitationJournal: Mol.Cell / Year: 2001
Title: Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis
Authors: Trincao, J. / Johnson, R.E. / Escalante, C.R. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: DNA Polymerase ETA
B: DNA Polymerase ETA


Theoretical massNumber of molelcules
Total (without water)116,3082
Polymers116,3082
Non-polymers00
Water9,296516
1
A: DNA Polymerase ETA


Theoretical massNumber of molelcules
Total (without water)58,1541
Polymers58,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA Polymerase ETA


Theoretical massNumber of molelcules
Total (without water)58,1541
Polymers58,1541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.100, 105.100, 292.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA Polymerase ETA /


Mass: 58153.750 Da / Num. of mol.: 2 / Fragment: Catalytic domain (residues 1-531)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD30 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04049
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20K, Ammonium Acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %PEG2000011
2600 mMammonium acetate11

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11631
21631
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 31-ID10.97958,0.97941,0.96482
SYNCHROTRONNSLS X4A20.96675
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJan 15, 2001
ADSC QUANTUM 42CCDDec 6, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1UndulatorMADMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979581
20.979411
30.964821
40.966751
ReflectionResolution: 2.25→50 Å / Num. all: 72278 / Num. obs: 68697 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 19 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.8
Reflection shellResolution: 2.25→50 Å / Redundancy: 19 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 17.8 / Num. unique all: 1335912 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 70064 / Num. measured all: 1335912
Reflection shell
*PLUS
% possible obs: 74 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→50 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 6979 -random
Rwork0.215 ---
all0.219 78627 --
obs0.214 68697 87.4 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.118 Å20 Å20 Å2
2---1.118 Å20 Å2
3---2.235 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7894 0 0 516 8410
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.265
X-RAY DIFFRACTIONc_mcbond_it1.3371.5
X-RAY DIFFRACTIONc_scbond_it2.2652
X-RAY DIFFRACTIONc_mcangle_it2.1742
X-RAY DIFFRACTIONc_scangle_it3.2042.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 2 / Rfactor obs: 0.226 / Rfactor Rfree: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5

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