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- PDB-6dlk: Crystal structure of DNA polymerase III subunit beta from Rickett... -

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Basic information

Entry
Database: PDB / ID: 6dlk
TitleCrystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii
ComponentsBeta sliding clamp
KeywordsTRANSFERASE / SSGCID / DnaN / DNA polymerase III beta / potential drug target / sliding clamp / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesRickettsia rickettsii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of DNA polymerase III subunit beta from Rickettsia rickettsii
Authors: Conrady, D.G. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0106
Polymers86,7612
Non-polymers2484
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-4 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.090, 97.570, 115.830
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 Beta sliding clamp


Mass: 43380.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (strain Sheila Smith) (bacteria)
Strain: Sheila Smith / Gene: A1G_03290 / Plasmid: RiriA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AWV3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Rigaku Reagents Top96 G6: (0.5 M Ammonium Sulfate, 0.1 M Sodium Citrate:Citric Acid pH 5.6, 1 M Lithium Sulfate) mixed 1:1 with 20 mg/mL protein in sitting drop vapor diffusion. Tray id ...Details: Rigaku Reagents Top96 G6: (0.5 M Ammonium Sulfate, 0.1 M Sodium Citrate:Citric Acid pH 5.6, 1 M Lithium Sulfate) mixed 1:1 with 20 mg/mL protein in sitting drop vapor diffusion. Tray id 291006g9, crystal id qtv9-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017 / Details: Beryllium Lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→36.649 Å / Num. obs: 60964 / % possible obs: 99.6 % / Redundancy: 6.037 % / Biso Wilson estimate: 30.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 1.048 / Net I/σ(I): 22.18 / Num. measured all: 368066
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.055.6480.5843.144620.8450.644100
2.05-2.116.1830.4434.4743760.9270.484100
2.11-2.176.2040.3455.7942210.950.377100
2.17-2.246.1960.287.1341290.9630.306100
2.24-2.316.1910.2288.7139960.9770.249100
2.31-2.396.1740.19210.4138580.9820.2199.9
2.39-2.486.1910.16111.9937570.9890.176100
2.48-2.586.1770.12814.9236030.9920.1499.9
2.58-2.76.1470.10317.9234660.9940.11299.9
2.7-2.836.1250.0822.333160.9960.08799.9
2.83-2.986.1370.06526.1231460.9970.07199.6
2.98-3.166.0410.05232.5929820.9980.05799.5
3.16-3.385.9970.03940.0428000.9990.04399.4
3.38-3.655.9150.03344.8526150.9990.03799.3
3.65-45.8470.0348.6924180.9990.03398.9
4-4.475.7490.02753.2821870.9990.02998.6
4.47-5.165.7620.02455.2719380.9990.02698.5
5.16-6.325.8010.02653.2616510.9990.02898.3
6.32-8.945.6780.02256.2513060.9990.02497.5
8.94-36.6495.2710.01958.9373710.02195

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TSZ

4tsz


Resolution: 2→36.649 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 1976 3.24 %
Rwork0.1666 --
obs0.168 60951 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→36.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 16 537 6266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155866
X-RAY DIFFRACTIONf_angle_d1.2017980
X-RAY DIFFRACTIONf_dihedral_angle_d13.7583612
X-RAY DIFFRACTIONf_chiral_restr0.082982
X-RAY DIFFRACTIONf_plane_restr0.0081015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.3311540.2494136X-RAY DIFFRACTION100
2.05-2.10540.27631370.20624206X-RAY DIFFRACTION100
2.1054-2.16740.23561360.18354166X-RAY DIFFRACTION100
2.1674-2.23730.23281540.1754158X-RAY DIFFRACTION100
2.2373-2.31730.1831360.16694210X-RAY DIFFRACTION100
2.3173-2.410.22961500.16444173X-RAY DIFFRACTION100
2.41-2.51970.21061450.16634198X-RAY DIFFRACTION100
2.5197-2.65250.22581310.16894196X-RAY DIFFRACTION100
2.6525-2.81860.23371470.17174207X-RAY DIFFRACTION100
2.8186-3.03620.22851230.17984248X-RAY DIFFRACTION100
3.0362-3.34150.24941580.17424188X-RAY DIFFRACTION99
3.3415-3.82460.19821450.16944224X-RAY DIFFRACTION99
3.8246-4.81690.16691220.13584277X-RAY DIFFRACTION99
4.8169-36.65540.18211380.16044388X-RAY DIFFRACTION98
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)Origin x (Å)Origin y (Å)Origin z (Å)
11.2274-0.8393-0.13051.5150.30740.6754-0.0653-0.05990.06190.11680.0682-0.02730.06470.0909-0.00560.20880.0012-0.01420.2259-0.00780.198110.492319.213-3.8959
22.0553-0.4064-0.84422.39980.31772.4142-0.00170.1002-0.2578-0.0331-0.0843-0.08230.44070.31480.07290.22580.0976-0.02710.2623-0.00250.206524.4652-0.8333-12.5693
30.8186-0.3972-0.161.666-1.46131.75990.08640.1180.0081-0.5096-0.4954-0.4790.67621.04990.23410.45280.27710.12440.67560.06350.379737.44373.3687-35.354
42.3042-1.74390.8746.9355-1.91964.37030.04810.40180.0236-0.3937-0.2609-0.09980.08020.50660.17860.29160.0560.09820.34780.0790.34328.135824.8097-53.0433
52.7228-1.1705-1.08311.81620.15172.1740.08250.0819-0.0285-0.1247-0.0576-0.1260.0190.05-0.02410.28810.008-0.03680.20430.01850.28128.391445.7658-45.8926
61.03110.3632-0.38652.2735-1.52134.2419-0.0073-0.04540.12950.15150.04650.0827-0.4259-0.1288-0.03040.22150.0348-0.02880.193-0.00380.23161.931347.1867-18.3302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 140 )
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 379 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 115 )
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 257 )
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 379 )

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