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- PDB-1em8: Crystal structure of chi and psi subunit heterodimer from DNA POL III -

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Basic information

Entry
Database: PDB / ID: 1em8
TitleCrystal structure of chi and psi subunit heterodimer from DNA POL III
Components
  • DNA POLYMERASE III CHI SUBUNIT
  • DNA POLYMERASE III PSI SUBUNIT
KeywordsGENE REGULATION / DNA Pol III / heterodimer / clamp-loader / alpha-beta fold
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / positive regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / response to radiation / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding
Similarity search - Function
DNA polymerase III subunit chi / DNA polymerase III, psi subunit / DNA polymerase III chi subunit, HolC / DNA polymerase III subunit chi superfamily / DNA polymerase III chi subunit, HolC / DNA polymerase III, psi subunit / DNA polymerase III, psi subunit, subgroup / DNA polymerase III, psi subunit superfamily / DNA polymerase III psi subunit / Rossmann fold ...DNA polymerase III subunit chi / DNA polymerase III, psi subunit / DNA polymerase III chi subunit, HolC / DNA polymerase III subunit chi superfamily / DNA polymerase III chi subunit, HolC / DNA polymerase III, psi subunit / DNA polymerase III, psi subunit, subgroup / DNA polymerase III, psi subunit superfamily / DNA polymerase III psi subunit / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit psi / DNA polymerase III subunit chi
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGulbis, J.M. / Finkelstein, J. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex.
Authors: Gulbis, J.M. / Kazmirski, S.L. / Finkelstein, J. / Kelman, Z. / O'Donnell, M. / Kuriyan, J.
History
DepositionMar 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: 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 III CHI SUBUNIT
B: DNA POLYMERASE III PSI SUBUNIT
C: DNA POLYMERASE III CHI SUBUNIT
D: DNA POLYMERASE III PSI SUBUNIT


Theoretical massNumber of molelcules
Total (without water)57,7154
Polymers57,7154
Non-polymers00
Water4,612256
1
A: DNA POLYMERASE III CHI SUBUNIT
B: DNA POLYMERASE III PSI SUBUNIT


Theoretical massNumber of molelcules
Total (without water)28,8582
Polymers28,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area12860 Å2
MethodPISA
2
C: DNA POLYMERASE III CHI SUBUNIT
D: DNA POLYMERASE III PSI SUBUNIT


Theoretical massNumber of molelcules
Total (without water)28,8582
Polymers28,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.377, 65.719, 73.429
Angle α, β, γ (deg.)90.0, 116.152, 90.0
Int Tables number4
Space group name H-MP1211
DetailsOne biological assembly is a heterodimer constructed from chain A and chain B / One biological assembly is a heterodimer constructed from chain C and chain D

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Components

#1: Protein DNA POLYMERASE III CHI SUBUNIT


Mass: 16653.742 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28905, DNA-directed DNA polymerase
#2: Protein DNA POLYMERASE III PSI SUBUNIT


Mass: 12203.835 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28632, DNA-directed DNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Fragment: WATER / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: methylpentanediol, HEPES, PEG 4000, Glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1reservoirpH7.5
34 mMdithiothreitol1reservoir
40.5 mMEDTA1reservoir
5100 mM1reservoirNaCl
610 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 223463 / Num. obs: 218771 / % possible obs: 97.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1 % / Rmerge(I) obs: 0.194 / Num. unique all: 4047 / % possible all: 95.2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 32326 / Num. measured all: 218771
Reflection shell
*PLUS
% possible obs: 95.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementResolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.265 3101 -random
Rwork0.229 ---
all0.233 30953 --
obs0.233 27852 97.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 0 256 4226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d3.2
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg3.2

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