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- PDB-4trt: Deinococcus radiodurans DNA polymerase III subunit beta -

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Basic information

Entry
Database: PDB / ID: 4trt
TitleDeinococcus radiodurans DNA polymerase III subunit beta
ComponentsDNA polymerase III subunit beta
KeywordsTRANSFERASE / DNA clamp
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNiiranen, L. / Lian, K. / Johnson, K.A. / Moe, E.
Funding support Norway, 1items
OrganizationGrant numberCountry
The Research Council of Norway Norway
CitationJournal: Bmc Struct.Biol. / Year: 2015
Title: Crystal structure of the DNA polymerase III beta subunit ( beta-clamp) from the extremophile Deinococcus radiodurans.
Authors: Niiranen, L. / Lian, K. / Johnson, K.A. / Moe, E.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)79,0872
Polymers79,0872
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-7 kcal/mol
Surface area32040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.410, 84.410, 198.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA polymerase III subunit beta


Mass: 39543.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The last seven residues are not visible in the electron density. The last six residues are cloning artefacts. The Uniprot entry Q9RYE8 sequence is incorrect due to an annotation mistake in ...Details: The last seven residues are not visible in the electron density. The last six residues are cloning artefacts. The Uniprot entry Q9RYE8 sequence is incorrect due to an annotation mistake in the genomic sequence leading to a frameshift. This is corrected in our sequence giving a protein of 362 aa.
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0001 / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star pLysS pRARE / References: UniProt: Q9RYE8, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe last six residues are cloning artefacts. The Uniprot entry Q9RYE8 sequence is incorrect due to ...The last six residues are cloning artefacts. The Uniprot entry Q9RYE8 sequence is incorrect due to an annotation mistake in the genomic sequence leading to a frameshift. This is corrected in our sequence giving a protein of 362 aa.

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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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 21% PEG 5000 MME, 0.12 M TRIS, 3.6% HEXANEDIOL / Temp details: RT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2011
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 55287 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 40.228 Å2 / Rmerge F obs: 0.107 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.053 / Χ2: 1.019 / Net I/σ(I): 17.37 / Num. measured all: 184746
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.053.30.7280.5282.613431410740320.62398.2
2.05-2.110.5470.423.4113741401839860.49399.2
2.11-2.170.4250.3424.2413260389238530.40299
2.17-2.240.3540.2914.9512814378637500.34399
2.24-2.310.2780.2176.3512166367236120.25798.4
2.31-2.390.2410.1857.1911244356734400.2296.4
2.39-2.480.1920.1558.3411274346833880.18397.7
2.48-2.580.1480.12210.3411347329532710.14399.3
2.58-2.70.1070.09412.9410917319031690.1199.3
2.7-2.830.0950.07714.9810305305430330.09299.3
2.83-2.980.0710.05818.839631292028880.06998.9
2.98-3.160.0540.04422.488239274226010.05294.9
3.16-3.380.0380.03428.988842262825920.0498.6
3.38-3.650.0290.02735.538058242923770.03297.9
3.65-40.0230.02340.447287224622080.02798.3
4-4.470.020.01944.26052204619570.02495.7
4.47-5.160.0150.01649.085495181017470.0296.5
5.16-6.320.0170.01748.645064155915200.0297.5
6.32-8.940.0160.01648.733507123611910.0296.4
8.940.0120.01458.5720727386720.01791.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
Cootmodel building
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2POL

2pol


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.183 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 2806 5.1 %RANDOM
Rwork0.1981 52481 --
obs0.2 55287 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 100.01 Å2 / Biso mean: 39.442 Å2 / Biso min: 26.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5432 0 0 292 5724
Biso mean---49.16 -
Num. residues----722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195550
X-RAY DIFFRACTIONr_bond_other_d0.0030.023758
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9827520
X-RAY DIFFRACTIONr_angle_other_deg0.99639170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10924.05242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42115938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.41546
X-RAY DIFFRACTIONr_chiral_restr0.0780.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216302
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021104
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 204 -
Rwork0.266 3559 -
all-3763 -
obs--97.94 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.1968-1.08990.06444.56050.06221.47170.11080.17250.2227-0.2532-0.0542-0.1559-0.13760.0402-0.05660.0588-0.00240.0010.1209-0.01720.0494Chain A domain 23.299442.748743.4358
23.40990.3262-0.29452.0660.2271.7042-0.0622-0.3014-0.10960.1834-0.01720.02150.05430.05230.07940.04710.02260.0120.04360.0150.008Chain A domain 30.052115.187444.5949
33.8416-0.4578-1.65821.63660.82153.0224-0.0752-0.0277-0.4201-0.0322-0.0198-0.05060.13880.00530.09490.0456-0.00090.01250.10750.03450.1161Chain B domain 1-27.00236.276953.6247
42.2158-0.5955-0.05354.5064-0.54131.97170.00810.0778-0.23350.0074-0.03990.16860.1154-0.07210.03190.016-0.0273-0.00560.1110.00810.0344Chain B domain 2-50.965423.638157.0073
52.99650.9185-0.34352.792-0.51092.15450.0896-0.18780.09940.2419-0.04440.2363-0.1077-0.0945-0.04510.03870.01620.02610.03690.00090.0221Chain B domain 3-48.731350.584450.7007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A121 - 243
2X-RAY DIFFRACTION2A144 - 361
3X-RAY DIFFRACTION3B2 - 120
4X-RAY DIFFRACTION4B121 - 243
5X-RAY DIFFRACTION5B244 - 361

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