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- PDB-7rzm: Crystal Structure of dnaN DNA polymerase III beta subunit from St... -

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Basic information

Entry
Database: PDB / ID: 7rzm
TitleCrystal Structure of dnaN DNA polymerase III beta subunit from Stenotrophomonas maltophilia K279a
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsDNA BINDING PROTEIN / dnaA / Stenotrophomonas maltophilia / DNA polymerase III beta subunit / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of dnaN DNA polymerase III beta subunit from Stenotrophomonas maltophilia K279a
Authors: Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit beta


Theoretical massNumber of molelcules
Total (without water)41,8391
Polymers41,8391
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.960, 160.960, 36.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme / Beta sliding clamp


Mass: 41839.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: dnaN, Smlt0002 / Plasmid: StmaA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2FT80
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MORPHEUS F5 (321505f5): 100 mM MOPS/HEPES-Na pH 7.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20mM D-xylose, 20 mM N-acetyl-D-glucosamine, 10% (w/v) PEG 20000, ...Details: MORPHEUS F5 (321505f5): 100 mM MOPS/HEPES-Na pH 7.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20mM D-xylose, 20 mM N-acetyl-D-glucosamine, 10% (w/v) PEG 20000, 20% (v/v) PEG MME 550, 16.74 mg/mL StmaA.17987.a.B1.PS38645, direct cryo

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 15, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→46.47 Å / Num. obs: 29740 / % possible obs: 99.9 % / Redundancy: 5.009 % / Biso Wilson estimate: 35.981 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.087 / Χ2: 0.92 / Net I/σ(I): 16.99 / Num. measured all: 148980
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.215.0210.5862.9410956218121820.8410.655100
2.21-2.275.0960.4963.5310870213321330.8910.554100
2.27-2.335.0130.4324.0810076201120100.9140.483100
2.33-2.45.0570.3494.9210347204720460.9390.39100
2.4-2.485.060.2876.059726192219220.9580.32100
2.48-2.575.0470.2377.089604190419030.9740.26599.9
2.57-2.675.0640.2048.269040178517850.9760.228100
2.67-2.785.0220.16310.188970178717860.9860.18299.9
2.78-2.95.0650.12812.918393165816570.990.14399.9
2.9-3.045.0010.10115.848157163116310.9940.113100
3.04-3.215.050.07720.37625151115100.9960.08699.9
3.21-3.44.9960.05725.947329146714670.9980.064100
3.4-3.634.9920.04730.756864137513750.9980.053100
3.63-3.934.9870.0434.526413128712860.9980.04599.9
3.93-4.34.9910.03438.25850117311720.9990.03899.9
4.3-4.814.9530.02844.485320107410740.9990.031100
4.81-5.554.8960.0342.3447309669660.9990.034100
5.55-6.84.9080.03138.5540208228190.9990.03599.6
6.8-9.624.7730.02544.91307464464410.028100
9.62-46.474.3440.02149.3416163823720.9990.02497.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tsz

4tsz


Resolution: 2.15→46.47 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2078 6.99 %
Rwork0.1683 27657 -
obs0.1719 29735 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.61 Å2 / Biso mean: 35.6982 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 2.15→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 0 354 3179
Biso mean---42.82 -
Num. residues----367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20.26341320.212718091941100
2.2-2.250.26131480.197518321980100
2.26-2.320.26321130.197518131926100
2.32-2.380.31361220.194918741996100
2.38-2.460.22941280.183318171945100
2.46-2.550.231260.182118421968100
2.55-2.650.2591400.189818191959100
2.65-2.770.2471600.186518281988100
2.77-2.920.25521530.193117971950100
2.92-3.10.26151310.184318631994100
3.1-3.340.25041410.169518431984100
3.34-3.680.21051310.158618621993100
3.68-4.210.19281410.141918511992100
4.21-5.30.16511710.124318502021100
5.3-46.470.19021410.17761957209899
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)
15.2629-0.44421.28652.29950.64273.844-0.0663-0.0320.08750.02740.0384-0.0743-0.09470.05870.07080.17360.02310.03340.13850.0190.1443-42.946-41.7014-1.0735
21.1154-0.8601-0.83040.94820.40362.02010.0228-0.76340.59360.09160.062-0.2974-0.2968-0.02260.10570.3137-0.02450.00290.1741-0.04280.3409-41.023-39.02115.1826
32.4159-1.90730.39293.8212-0.39140.94310.0021-0.00160.20530.06420.0624-0.2791-0.07830.0903-0.04750.1855-0.0235-0.01510.215-0.01820.17-16.0672-54.3590.7995
43.02621.9799-0.85563.7523-0.07621.79070.0234-0.0151-0.15680.05110.0246-0.1088-0.0113-0.018-0.05490.16490.0244-0.04030.171-0.03390.1643-13.4525-81.2601-0.4471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 100 )A0 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 124 )A101 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 253 )A125 - 253
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 366 )A254 - 366

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