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- PDB-8dt6: Crystal Structure of DNA Polymerase III beta subunit from Elizabe... -

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Basic information

Entry
Database: PDB / ID: 8dt6
TitleCrystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis
ComponentsBeta sliding clamp
KeywordsDNA BINDING PROTEIN / SSGCID / Beta sliding clamp / DNA replication / DNA-binding / Transferase / Nucleotidyltransferase / DNA-directed DNA polymerase / 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 speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)172,43217
Polymers171,9544
Non-polymers47813
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-159 kcal/mol
Surface area62310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.410, 88.010, 100.240
Angle α, β, γ (deg.)90.000, 95.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 22 or (resid 27...
21(chain B and (resid 1 through 22 or (resid 27...
31(chain C and (resid 1 through 22 or (resid 27...
41(chain D and (resid 1 through 22 or resid 27...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 22 or (resid 27...A1 - 22
121(chain A and (resid 1 through 22 or (resid 27...A27
131(chain A and (resid 1 through 22 or (resid 27...A1 - 374
141(chain A and (resid 1 through 22 or (resid 27...A1 - 374
151(chain A and (resid 1 through 22 or (resid 27...A1 - 374
161(chain A and (resid 1 through 22 or (resid 27...A1 - 374
211(chain B and (resid 1 through 22 or (resid 27...B1 - 22
221(chain B and (resid 1 through 22 or (resid 27...B27
231(chain B and (resid 1 through 22 or (resid 27...B1 - 381
241(chain B and (resid 1 through 22 or (resid 27...B1 - 381
251(chain B and (resid 1 through 22 or (resid 27...B1 - 381
261(chain B and (resid 1 through 22 or (resid 27...B1 - 381
311(chain C and (resid 1 through 22 or (resid 27...C1 - 22
321(chain C and (resid 1 through 22 or (resid 27...C27
331(chain C and (resid 1 through 22 or (resid 27...C1 - 381
341(chain C and (resid 1 through 22 or (resid 27...C1 - 381
351(chain C and (resid 1 through 22 or (resid 27...C1 - 381
361(chain C and (resid 1 through 22 or (resid 27...C1 - 381
411(chain D and (resid 1 through 22 or resid 27...D1 - 22
421(chain D and (resid 1 through 22 or resid 27...D27 - 37
431(chain D and (resid 1 through 22 or resid 27...D38
441(chain D and (resid 1 through 22 or resid 27...D1 - 406
451(chain D and (resid 1 through 22 or resid 27...D1 - 406
461(chain D and (resid 1 through 22 or resid 27...D1 - 406

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Components

#1: Protein
Beta sliding clamp


Mass: 42988.617 Da / Num. of mol.: 4 / Fragment: ElanA.17987.a.AE1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_1355 / Plasmid: ElanA.17987.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077EHW1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: [Target: ElanA.17987.a.AE1.PS38659 - 28.82 mg/mL] [Barcode: 321211c7] [Pin: mjs7-5] [Crystallization: sparse screen - MCSG1 C7 - 100 mM Tris:HCl pH 8.5, 200 mM Calcium chloride, 25% (w/v) ...Details: [Target: ElanA.17987.a.AE1.PS38659 - 28.82 mg/mL] [Barcode: 321211c7] [Pin: mjs7-5] [Crystallization: sparse screen - MCSG1 C7 - 100 mM Tris:HCl pH 8.5, 200 mM Calcium chloride, 25% (w/v) PEG 4000, 14C, 0.2:0.2 drop ratio] [Cryo: 15% EG]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.35→40.26 Å / Num. obs: 66682 / % possible obs: 99.8 % / Redundancy: 4.213 % / Biso Wilson estimate: 44.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.059 / Χ2: 0.926 / Net I/σ(I): 18.5 / Num. measured all: 280947 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.414.2360.5482.7349220.8180.62699.8
2.41-2.484.240.4423.4147590.8650.50699.9
2.48-2.554.2380.3574.1846880.9090.408100
2.55-2.634.2470.2974.9845020.9340.3499.9
2.63-2.714.2530.2426.1143940.9550.276100
2.71-2.814.2390.1937.642310.9730.22199.7
2.81-2.914.2390.1489.7740960.9820.16999.9
2.91-3.034.2330.11512.4139620.9890.131100
3.03-3.174.2380.08516.0937710.9940.09799.7
3.17-3.324.2170.06320.6836270.9970.07399.8
3.32-3.54.220.0525.5234200.9980.05799.8
3.5-3.724.1950.0430.0832790.9980.046100
3.72-3.974.1860.03633.3430590.9980.042100
3.97-4.294.1830.03137.3728540.9990.03699.8
4.29-4.74.2040.02642.4826260.9990.029100
4.7-5.254.180.02543.3924030.9990.029100
5.25-6.074.1680.02740.7521210.9990.03199.9
6.07-7.434.1250.02642.1317930.9990.03100
7.43-10.514.0850.02148.4114070.9990.02499.9
10.51-40.263.7630.02248.977680.9990.02596.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.35→40.26 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 2024 3.04 %
Rwork0.176 64642 -
obs0.1773 66666 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.98 Å2 / Biso mean: 54.4007 Å2 / Biso min: 27.47 Å2
Refinement stepCycle: final / Resolution: 2.35→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 13 513 11906
Biso mean--61.99 52.23 -
Num. residues----1494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6663X-RAY DIFFRACTION8.462TORSIONAL
12B6663X-RAY DIFFRACTION8.462TORSIONAL
13C6663X-RAY DIFFRACTION8.462TORSIONAL
14D6663X-RAY DIFFRACTION8.462TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.410.29361370.239246234760100
2.41-2.470.28231450.227545514696100
2.47-2.550.31281410.220246274768100
2.55-2.630.28061380.219745814719100
2.63-2.720.27561520.222446124764100
2.72-2.830.30581220.224746214743100
2.83-2.960.30821440.221246084752100
2.96-3.120.24941370.210146024739100
3.12-3.310.26751630.205245824745100
3.31-3.570.23471520.178746104762100
3.57-3.930.18471660.156945944760100
3.93-4.490.17791530.137946084761100
4.49-5.660.15151170.130546954812100
5.66-40.260.18731570.16784728488599
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)
12.44891.2972-0.40096.7664-1.69583.1915-0.05160.01880.11560.72070.07620.1379-0.5194-0.1482-0.0090.5650.05280.02270.46570.03330.2543-41.4912-22.6105-24.7914
21.6370.8046-1.02741.7214-0.77693.0080.2666-0.3966-0.00630.875-0.3076-0.2615-1.12240.26680.04350.9188-0.069-0.16680.4656-0.01580.3846-30.54640.5158-42.0587
32.5441-1.479-1.60153.26631.18032.42410.00310.0840.14430.172-0.0599-0.6774-0.42550.17480.03960.4681-0.1318-0.15910.48710.07140.5434-13.9448-4.7013-62.2024
43.1114-0.4235-0.16947.5172-2.74463.9667-0.10340.33310.0601-0.0674-0.1914-0.37060.07980.21150.27550.2517-0.03090.00480.42060.02970.3138-2.3359-33.3399-65.1023
53.13840.8806-1.58132.2347-1.38174.7781-0.30980.3563-0.2116-0.37560.0491-0.33650.4886-0.01720.2080.3727-0.0070.06110.3028-0.03410.321-14.3753-56.0056-49.2629
62.3529-0.86340.52082.70460.29182.5685-0.1483-0.0160.0189-0.08860.09350.0385-0.1043-0.11440.04130.3103-0.0920.01420.35610.00180.2284-33.3656-51.829-31.366
72.775-1.1057-0.54476.93651.70073.50440.0769-0.16050.09320.1306-0.00430.3583-0.1041-0.1069-0.07880.2028-0.01120.00790.29760.0390.3628-39.3438-30.000612.6713
82.2879-0.7799-1.67222.28050.37753.4028-0.0701-0.090.03070.04640.1016-0.041-0.05320.1033-0.05470.3064-0.0193-0.03890.2541-0.02650.3403-23.4882-53.2952-0.8983
91.84310.4935-0.70491.8241-0.02944.2920.0135-0.01550.1497-0.10850.0521-0.1640.06710.3183-0.07240.2620.01490.02360.3177-0.04240.4018-4.8453-49.4481-18.8658
102.5913-3.88793.27617.6538-2.71887.5138-0.0674-0.4002-0.1953-0.01180.11010.1827-0.4183-0.03160.00320.4093-0.10830.19180.3409-0.0570.4434-1.5205-18.5862-25.2767
111.6278-1.72810.37395.74320.33321.56510.08840.1181-0.1032-0.5078-0.0235-0.4632-0.04250.2131-0.05170.3779-0.07510.14530.4057-0.0520.46412.1813-20.2709-27.9829
125.5983-0.9286-3.69665.02840.74665.7850.01160.2066-0.1784-0.2978-0.00160.0850.0398-0.27870.12560.342-0.0081-0.0010.3034-0.00820.323-14.05271.0942-11.7628
135.0491-0.8107-4.19553.08171.734.74110.03710.1330.0251-0.35740.0614-0.3875-0.23440.0192-0.11620.3424-0.02180.04390.31660.01490.3086-11.23993.8906-12.2449
143.15181.191-0.94285.3529-1.50713.42460.12020.06760.00430.3127-0.03650.3205-0.170.0208-0.09280.23050.026-0.00460.2949-0.0130.2995-29.7387-1.59267.3215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )A1 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 257 )A130 - 257
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 374 )A258 - 374
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 129 )B1 - 129
5X-RAY DIFFRACTION5chain 'B' and (resid 130 through 257 )B130 - 257
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 381 )B258 - 381
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 129 )C1 - 129
8X-RAY DIFFRACTION8chain 'C' and (resid 130 through 257 )C130 - 257
9X-RAY DIFFRACTION9chain 'C' and (resid 258 through 381 )C258 - 381
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 38 )D1 - 38
11X-RAY DIFFRACTION11chain 'D' and (resid 39 through 129 )D39 - 129
12X-RAY DIFFRACTION12chain 'D' and (resid 130 through 166 )D130 - 166
13X-RAY DIFFRACTION13chain 'D' and (resid 167 through 257 )D167 - 257
14X-RAY DIFFRACTION14chain 'D' and (resid 258 through 376 )D258 - 376

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