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- PDB-6djk: Structure of DNA polymerase III subunit beta from Rickettsia typh... -

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Basic information

Entry
Database: PDB / ID: 6djk
TitleStructure of DNA polymerase III subunit beta from Rickettsia typhi in complex with a natural product
Components
  • ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
  • Beta sliding clamp
KeywordsDNA BINDING PROTEIN/INHIBITOR / SSGCID / BETA SLIDING CLAMP / DNAN / DNA POLYMERASE III SUBUNIT BETA / GRISELMYCIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / TRANSFERASE-PEPTIDE complex / DNA BINDING PROTEIN-INHIBITOR complex
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
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / DI(HYDROXYETHYL)ETHER / Beta sliding clamp
Similarity search - Component
Biological speciesRickettsia typhi str. Wilmington (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of DNA polymerase III subunit beta from Rickettsia typhi in complex with a natural product
Authors: Abendroth, J. / Conrady, D.G. / Higgins, T.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
B: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2485
Polymers45,0182
Non-polymers2303
Water4,414245
1
A: Beta sliding clamp
B: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
hetero molecules

A: Beta sliding clamp
B: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,49710
Polymers90,0364
Non-polymers4616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area5480 Å2
ΔGint-20 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.500, 43.730, 83.900
Angle α, β, γ (deg.)90.000, 121.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta sliding clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / ...Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / DNA polymerase III subunit beta


Mass: 43902.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia typhi str. Wilmington (bacteria)
Strain: ATCC VR-144 / Wilmington / Gene: dnaN, RT0405 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q68WW0
#2: Protein/peptide ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Anatrace TOP96 screen, D10: 25 % (w/v) PEG 3350, 200mM Lithium Sulfate, 100mM Bis-Tris: HCl, pH 6.5: RifeA.17987.a.B1.PW38224 at 20mg/ml: soaked for 3.5h with 2.5mM Griselmycin: cryo: 15% EG ...Details: Anatrace TOP96 screen, D10: 25 % (w/v) PEG 3350, 200mM Lithium Sulfate, 100mM Bis-Tris: HCl, pH 6.5: RifeA.17987.a.B1.PW38224 at 20mg/ml: soaked for 3.5h with 2.5mM Griselmycin: cryo: 15% EG + soak buffer: tray 21006D10: puck WUA6-4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→38.766 Å / Num. obs: 39292 / % possible obs: 99.4 % / Redundancy: 3.328 % / Biso Wilson estimate: 29.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.043 / Χ2: 1.021 / Net I/σ(I): 19.59 / Num. measured all: 130762
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
1.85-1.93.3120.4942.739609291029010.8890.58999.7
1.9-1.953.3460.3743.719399281428090.9190.44499.8
1.95-2.013.3450.2844.779143274227330.9470.33899.7
2.01-2.073.3580.2186.159024269126870.9720.25999.9
2.07-2.143.3570.1538.478595257325600.9860.18299.5
2.14-2.213.3560.1279.968347250124870.9890.1599.4
2.21-2.293.3460.09712.468133243624310.9930.11599.8
2.29-2.393.3640.07914.557730230622980.9950.09499.7
2.39-2.493.3430.06916.587418223322190.9960.08299.4
2.49-2.623.3450.05719.917118214421280.9970.06899.3
2.62-2.763.3430.04623.226826205320420.9980.05599.5
2.76-2.933.3420.03827.636414193419190.9980.04599.2
2.93-3.133.3220.033326017182218110.9980.03999.4
3.13-3.383.3110.02637.25652171717070.9990.03199.4
3.38-3.73.3060.02342.335045154315260.9990.02798.9
3.7-4.143.3190.02146.864680142014100.9990.02599.3
4.14-4.783.280.01949.534143127012630.9990.02399.4
4.78-5.853.2570.01950.13482108310690.9990.02398.7
5.85-8.273.2040.0248.7926598398300.9990.02498.9
8.27-38.7662.8740.02150.513284954620.9990.02593.3

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Processing

Software
NameVersionClassification
PHENIXdev_3092refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5W7W-A AS PER MORDA

5w7w


Resolution: 1.85→38.766 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1904 4.85 %0
Rwork0.1729 ---
obs0.1747 39270 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.54 Å2 / Biso mean: 39.9195 Å2 / Biso min: 19.81 Å2
Refinement stepCycle: final / Resolution: 1.85→38.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 94 247 3271
Biso mean--47.68 45.87 -
Num. residues----376
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 (%)
1.85-1.89630.30821250.279226752800100
1.8963-1.94760.32281280.248226492777100
1.9476-2.00490.25641280.216826712799100
2.0049-2.06960.2571210.208326742795100
2.0696-2.14350.24511560.190826172773100
2.1435-2.22930.21621420.184926202762100
2.2293-2.33080.21281180.1826902808100
2.3308-2.45370.26231360.187426512787100
2.4537-2.60740.20481440.180226562800100
2.6074-2.80860.25021700.184126292799100
2.8086-3.09120.23031320.178126982830100
3.0912-3.53820.22321470.172426632810100
3.5382-4.45670.15741260.142927062832100
4.4567-38.77470.17071310.15342767289899
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)
17.8086-3.29845.13545.9122-0.72926.185-0.0418-0.1050.30890.2144-0.5511-0.5559-0.2515-0.49870.54280.3361-0.0138-0.00970.53540.19020.381124.260637.530839.3134
22.95771.52950.41813.3785-0.9264.80760.0509-0.3370.06370.105-0.1373-0.0858-0.0625-0.02770.08540.17180.0138-0.00540.2812-0.03420.183.723321.934880.5143
33.6124-0.7511-1.8011.22110.38394.11390.00820.26710.0269-0.0186-0.07620.02940.0648-0.24420.06590.17220.0025-0.01740.17930.00350.16998.481124.038152.3182
43.755-0.1021-0.2960.80560.02470.91070.0130.7942-0.0558-0.0263-0.0482-0.12040.04560.17430.04370.24160.0289-0.02240.39830.02770.191331.103321.141243.1409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1001 through 1011 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 0 through 115 )A0 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 230 )A116 - 230
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 381 )A231 - 381

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