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- PDB-5w7z: Crystal structure of DNA polymerase III subunit beta from Rickett... -

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Basic information

Entry
Database: PDB / ID: 5w7z
TitleCrystal structure of DNA polymerase III subunit beta from Rickettsia conorii
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / 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 speciesRickettsia conorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of DNA polymerase III subunit beta from Rickettsia conorii
Authors: Bowatte, K. / Conrady, D.G. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Derived calculations / Category: pdbx_struct_assembly / Item: _pdbx_struct_assembly.details
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,9346
Polymers86,6292
Non-polymers3044
Water16,592921
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint1 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.520, 86.910, 79.510
Angle α, β, γ (deg.)90.000, 115.390, 90.000
Int Tables number4
Space group name H-MP1211
DetailsDimer as determined by gel filtration

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme


Mass: 43314.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia conorii (strain ATCC VR-613 / Malish 7) (bacteria)
Strain: ATCC VR-613 / Malish 7 / Gene: dnaN, RC0583 / Plasmid: Rico.17987.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92I37, DNA-directed DNA polymerase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.77 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Rigaku Reagents Precipitant Synergy Screen 2, condition e8:2.01 %v/v MPD, 13.4%w/v PEG 8000, 100 mM Imidazole/Hydrochloric acid pH 6.5: RicoA.17987.a.B1.PW38227 at 20 mg/ml, cryo 20% EG, ...Details: Rigaku Reagents Precipitant Synergy Screen 2, condition e8:2.01 %v/v MPD, 13.4%w/v PEG 8000, 100 mM Imidazole/Hydrochloric acid pH 6.5: RicoA.17987.a.B1.PW38227 at 20 mg/ml, cryo 20% EG, tray 290986e8, puck sgk8-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→36.275 Å / Num. obs: 102967 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 21.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.052 / Χ2: 1.04 / Net I/σ(I): 17.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.743.1050.5642.1275800.760.68399.4
1.74-1.793.4240.4552.8573810.860.53899.6
1.79-1.843.4280.3293.9171890.9230.38999.5
1.84-1.93.4320.255.1470090.9510.29699.6
1.9-1.963.4380.181767800.9710.21499.5
1.96-2.033.4380.1369.0865810.9840.16199.7
2.03-2.113.4430.10111.6563160.990.1299.7
2.11-2.193.4340.08314.3660990.9930.09899.5
2.19-2.293.4450.07116.5358360.9940.08499.7
2.29-2.43.4370.05919.3656320.9960.0799.6
2.4-2.533.4370.05321.3652780.9960.06299.6
2.53-2.693.4320.04624.5150630.9970.05499.7
2.69-2.873.4280.0427.647550.9970.04799.4
2.87-3.13.4070.03431.443780.9980.0499.3
3.1-3.43.3750.0336.0540500.9980.03699.3
3.4-3.83.3450.02739.6936870.9980.03299.2
3.8-4.393.4070.02442.5832580.9990.02899.4
4.39-5.383.3970.02244.3227540.9990.02699.5
5.38-7.63.4410.02343.0821550.9990.02799
7.6-503.2960.0245.511860.9990.02497.1

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Processing

Software
NameVersionClassification
PHENIX1.12rc1_2807refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN entry: 4tszA

Resolution: 1.7→36.275 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 2000 1.94 %0, random
Rwork0.164 ---
obs0.1645 102941 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 29.5489 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 1.7→36.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 20 932 6746
Biso mean--44.65 39.71 -
Num. residues----761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066159
X-RAY DIFFRACTIONf_angle_d0.838414
X-RAY DIFFRACTIONf_chiral_restr0.0581031
X-RAY DIFFRACTIONf_plane_restr0.0051074
X-RAY DIFFRACTIONf_dihedral_angle_d13.0873915
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 (%)
1.7-1.74250.28561390.24571787317100
1.7425-1.78960.29031460.224871457291100
1.7896-1.84230.26191400.223171947334100
1.8423-1.90170.24621340.20772017335100
1.9017-1.96970.24461290.177772077336100
1.9697-2.04860.18891550.176471697324100
2.0486-2.14180.20571680.17372007368100
2.1418-2.25470.19561390.167572037342100
2.2547-2.39590.19661500.164471987348100
2.3959-2.58090.20011430.167371997342100
2.5809-2.84050.19271460.166172277373100
2.8405-3.25130.18971400.162872107350100
3.2513-4.09540.13671380.142672687406100
4.0954-36.28350.15811330.14387342747599
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)
11.4229-0.0019-0.48290.93080.46574.6493-0.0206-0.0362-0.09350.0025-0.0151-0.00080.1109-0.12660.03320.1079-0.0042-0.00140.1258-0.00410.1432-10.8235-1.185810.8713
22.25830.041.30570.5809-0.03573.20220.0233-0.1478-0.0430.00670.02130.03710.0283-0.1815-0.03550.1408-0.00170.0150.1162-0.00490.1583-4.98421.901138.8187
32.976-0.517-0.73860.90.06181.25220.0414-0.16570.12640.03130.0295-0.0374-0.13770.0795-0.05440.1428-0.0160.01010.1369-0.01780.136720.69090.769747.1153
41.68280.24-0.20892.14040.27352.6817-0.00160.0073-0.0059-0.00580.02510.11930.0414-0.0177-0.01720.09860.004-0.00090.110.01470.135638.6757-11.356928.4856
52.1456-0.48191.46670.5302-0.39023.09790.22070.4259-0.2148-0.088-0.15820.01170.34780.3531-0.03680.22520.0384-0.01570.2061-0.040.178633.4771-18.50190.8576
62.5998-0.6450.15321.077-0.24811.58140.08240.3575-0.0937-0.0561-0.08160.0450.01530.04730.01280.1375-0.0068-0.00470.2102-0.0330.11729.866-8.3922-10.8469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 125 )A0 - 125
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 257 )A126 - 257
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 379 )A258 - 379
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 115 )B-1 - 115
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 257 )B116 - 257
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 379 )B258 - 379

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