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- PDB-6dm6: Structure of DNA polymerase III subunit beta from Rickettsia cono... -

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Basic information

Entry
Database: PDB / ID: 6dm6
TitleStructure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a natural product
Components
  • Beta sliding clamp
  • Natural product peptide
KeywordsTRANSFERASE / SSGCID / dnaN / DNA polymerase III subunit beta / 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, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / :
Similarity search - Domain/homology
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / Beta sliding clamp
Similarity search - Component
Biological speciesRickettsia conorii (bacteria)
Streptomyces caelicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a natural product
Authors: Conrady, D.G. / Abendroth, J. / Higgins, T.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Structure summary
Category: pdbx_molecule_features / struct_site / struct_site_gen
Revision 1.2Oct 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 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: Beta sliding clamp
C: Natural product peptide
D: Natural product peptide


Theoretical massNumber of molelcules
Total (without water)88,8604
Polymers88,8604
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-26 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.860, 41.830, 127.400
Angle α, β, γ (deg.)90.000, 93.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 4 or (resid 5...
21(chain B and (resid -1 through 23 or resid 29...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISLEULEU(chain A and (resid -1 through 4 or (resid 5...AA-1 - 47 - 12
121ILEILEILEILE(chain A and (resid -1 through 4 or (resid 5...AA513
131HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
141HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
151HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
161HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
211HISHISGLUGLU(chain B and (resid -1 through 23 or resid 29...BB-1 - 237 - 31
221PROPROASPASP(chain B and (resid -1 through 23 or resid 29...BB29 - 5137 - 59
231TYRTYRVALVAL(chain B and (resid -1 through 23 or resid 29...BB53 - 7961 - 87
241HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
251HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
261HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
271HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
281HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
112ACEACEGLYGLYchain CCC1 - 111 - 11
212ACEACEGLYGLYchain DDD1 - 111 - 11

NCS ensembles :
ID
1
2

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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: 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: RicoA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92I37
#2: Protein/peptide Natural product peptide


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces caelicus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: Rigaku Wizard Cryo 1/2 A8: 0.1M Sodium cacodylate pH6.5, 35% 2-ethoxyethanol 0.4:0.4uL drops, direct cryo: tray 290984a8: puck mbp2-7

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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: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→49.017 Å / Num. obs: 42516 / % possible obs: 99.6 % / Redundancy: 3.725 % / Biso Wilson estimate: 36.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 1.022 / Net I/σ(I): 15.54 / Num. measured all: 158384 / Scaling rejects: 7
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
2.25-2.313.7750.5522.3911944317131640.8710.64599.8
2.31-2.373.7820.4562.8911315299529920.8880.53299.9
2.37-2.443.7840.4093.2911212296829630.9070.47899.8
2.44-2.523.7780.3443.8710908289028870.9220.40199.9
2.52-2.63.7860.2944.6410587279527960.9480.343100
2.6-2.693.780.2295.910160269826880.9630.26799.6
2.69-2.793.7790.197.139981264326410.9770.22299.9
2.79-2.93.7690.1518.789246246124530.9850.17699.7
2.9-3.033.7660.11811.319167244024340.9890.13899.8
3.03-3.183.7570.08514.728626230922960.9950.199.4
3.18-3.353.7280.06618.878167220321910.9960.07799.5
3.35-3.563.70.04823.967610206920570.9980.05699.4
3.56-3.83.6680.0427.97280199419850.9980.04699.5
3.8-4.113.6490.03232.46575181318020.9990.03899.4
4.11-4.53.6370.02638.176084168616730.9990.0399.2
4.5-5.033.650.02440.65599154315340.9990.02899.4
5.03-5.813.6150.02638.344945137613680.9990.03199.4
5.81-7.123.5510.02836.774137117211650.9990.03399.4
7.12-10.063.5010.01846.26318291690910.02199.2
10.06-49.0173.2030.01848.36165954251810.02195.6

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Processing

Software
NameVersionClassification
PHENIXdev_3126refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DLK

6dlk


Resolution: 2.25→49.017 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.87
RfactorNum. reflection% reflection
Rfree0.2348 1978 4.66 %
Rwork0.1783 --
obs0.181 42486 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.45 Å2 / Biso mean: 47.8618 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 2.25→49.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5867 0 0 301 6168
Biso mean---47.02 -
Num. residues----777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2186X-RAY DIFFRACTION5.58TORSIONAL
12B2186X-RAY DIFFRACTION5.58TORSIONAL
21C26X-RAY DIFFRACTION5.58TORSIONAL
22D26X-RAY DIFFRACTION5.58TORSIONAL
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 (%)
2.2501-2.30640.26221220.217429193041100
2.3064-2.36870.25371460.227128522998100
2.3687-2.43840.31561320.224628532985100
2.4384-2.51710.28111380.216228833021100
2.5171-2.60710.30791400.215628973037100
2.6071-2.71150.27531260.208128682994100
2.7115-2.83490.31771320.209328983030100
2.8349-2.98430.27761690.199328643033100
2.9843-3.17120.24721520.2092831298399
3.1712-3.4160.25121370.19012885302299
3.416-3.75970.24451360.17432923305999
3.7597-4.30350.20331350.15542896303199
4.3035-5.42080.18181570.1352922307999
5.4208-49.0290.19111560.15573017317399
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)
17.5458-3.282-0.63126.0428-0.1844.93120.03310.17920.1658-0.1152-0.10920.0873-0.2268-0.12880.10990.2014-0.0426-0.00330.19290.00020.205-1.47993.9137-12.3151
24.8044-0.8587-1.06150.65590.30141.7030.0625-0.03420.2537-0.0137-0.06780.0385-0.0545-0.04010.01880.2609-0.018-0.03630.13930.01860.2453-13.19976.0105-9.2736
31.88210.04570.64910.81950.43241.7878-0.0248-0.0653-0.08070.0017-0.05770.15760.025-0.4670.0770.2411-0.0150.03360.3162-0.03260.3205-38.11913.8163-13.7765
47.18240.0029-3.28397.3773-2.60125.9775-0.01440.07710.1718-0.3286-0.0499-0.1366-0.2696-0.07810.08660.33220.0286-0.04250.3962-0.12820.2925-37.45511.5432-51.0718
54.0591-0.1616-0.7997-0.0023-0.02541.35040.07810.61340.1442-0.1623-0.15990.0762-0.0858-0.09860.05870.43910.0698-0.03040.33430.00420.295-22.27242.1063-55.8584
65.95980.6366-0.26450.37430.30391.6062-0.01510.40860.2043-0.0898-0.00530.12470.05240.05630.06190.41710.07070.01280.39730.06210.3419-15.16771.5418-59.3598
71.9407-0.0261.08631.89860.96494.22420.16070.3898-0.1145-0.1293-0.0215-0.15630.25430.4474-0.14390.34560.09570.02950.41140.02460.24398.3917-1.2056-41.8054
84.07881.7725-1.48666.06222.19273.8342-0.1856-0.62140.50631.26950.4643-1.0453-0.67520.2418-0.24790.68410.1528-0.26790.4838-0.12730.6927-42.747520.4582-11.0026
94.867-1.0176-0.63185.5643-1.07792.8347-0.27030.90570.6792-1.4877-0.01060.684-0.9821-0.55190.12470.62780.0444-0.13880.60610.18510.41345.239315.6628-55.101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 81 )A-1 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 172 )A82 - 172
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 379 )A173 - 379
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 81 )B-1 - 81
5X-RAY DIFFRACTION5chain 'B' and (resid 82 through 191 )B82 - 191
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 257 )B192 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 379 )B258 - 379
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )C1 - 11
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 11 )D1 - 11

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