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- PDB-8cix: DNA-polymerase sliding clamp (DnaN) from Escherichia coli in comp... -

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Basic information

Entry
Database: PDB / ID: 8cix
TitleDNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Griselimycin.
Components
  • Beta sliding clamp
  • Griselimycin
KeywordsTRANSFERASE / DnaN / Sliding clamp / DNA-polymerase beta subunit / Antibiotic / Natural product / Anti-tuberculosis
Function / homology
Function and homology information


Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol
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
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / ACETATE ION / Beta sliding clamp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFu, C. / Liu, Y. / Walt, C. / Bader, C. / Rasheed, S. / Lukat, P. / Neuber, M. / Blankenfeldt, W. / Kalinina, O. / Mueller, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins.
Authors: Fu, C. / Liu, Y. / Walt, C. / Rasheed, S. / Bader, C.D. / Lukat, P. / Neuber, M. / Haeckl, F.P.J. / Blankenfeldt, W. / Kalinina, O.V. / Muller, R.
History
DepositionFeb 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
B: Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,77922
Polymers42,0172
Non-polymers76220
Water6,792377
1
A: Beta sliding clamp
B: Griselimycin
hetero molecules

A: Beta sliding clamp
B: Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,55844
Polymers84,0354
Non-polymers1,52440
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Unit cell
Length a, b, c (Å)83.936, 150.561, 71.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 40901.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN, b3701, JW3678 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A988
#2: Protein/peptide Griselimycin


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces griseus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY

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Non-polymers , 6 types, 397 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.36 M CaCl2 0.13 M MgCl2 0.24 M Na Acetate 8.3 % (v/v) Glycerol 12.2 % (w/v) PEG 3350 0.1 M HEPES/NaOH 7.7 Cryoprotection: 10 % (v/v) (2R,3R)-2,3-butanediol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.76→75.28 Å / Num. obs: 45185 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.088 / Χ2: 0.93 / Net I/σ(I): 17.9 / Num. measured all: 604946
Reflection shellResolution: 1.76→1.86 Å / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 1.03 / Num. measured all: 89664 / Num. unique obs: 6526 / CC1/2: 0.902 / Rpim(I) all: 0.288 / Rrim(I) all: 1.069 / Χ2: 0.79 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→51.88 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 2420 5.36 %
Rwork0.1787 --
obs0.1801 45163 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→51.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 113 377 3283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013148
X-RAY DIFFRACTIONf_angle_d1.0354315
X-RAY DIFFRACTIONf_dihedral_angle_d14.7471274
X-RAY DIFFRACTIONf_chiral_restr0.062507
X-RAY DIFFRACTIONf_plane_restr0.01571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.41560.3082490X-RAY DIFFRACTION100
1.8-1.840.28211510.26742487X-RAY DIFFRACTION100
1.84-1.880.26631520.21662450X-RAY DIFFRACTION100
1.88-1.930.23851630.19372455X-RAY DIFFRACTION100
1.93-1.980.21411210.18512485X-RAY DIFFRACTION100
1.98-2.040.22711350.19162534X-RAY DIFFRACTION100
2.04-2.10.22941470.20572474X-RAY DIFFRACTION100
2.1-2.180.2321470.17172461X-RAY DIFFRACTION100
2.18-2.270.19851310.16462515X-RAY DIFFRACTION100
2.27-2.370.21461280.17132516X-RAY DIFFRACTION100
2.37-2.490.21971230.17942529X-RAY DIFFRACTION100
2.49-2.650.21681230.18552523X-RAY DIFFRACTION100
2.65-2.850.22541580.19362512X-RAY DIFFRACTION100
2.85-3.140.19851410.1742528X-RAY DIFFRACTION100
3.14-3.60.20581350.16842564X-RAY DIFFRACTION100
3.6-4.530.16361490.1392558X-RAY DIFFRACTION100
4.53-51.880.17961600.19112662X-RAY DIFFRACTION100
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)
12.83330.17980.3940.48590.16750.7017-0.0858-0.10890.30690.02850.03780.027-0.04940.06760.03010.24090.02290.01060.22750.03170.253122.125127.270217.3186
20.83420.1189-0.41561.5512-0.17240.76440.0347-0.04640.0591-0.0354-0.0250.0486-0.0338-0.0043-0.00780.17560.0042-0.00390.2050.01350.180297.771110.515218.1653
32.2147-0.53740.31250.2514-0.0716-0.0429-0.01290.00640.19210.02140.0113-0.0407-0.0168-0.01090.00270.21820.00820.00480.2064-0.00140.1941136.483821.616718.5821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 197 through 253 )
2X-RAY DIFFRACTION2chain 'A' and (resid 254 through 366 )
3X-RAY DIFFRACTION3chain 'A' and (resid -1 through 196 )

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