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

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Basic information

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


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L34 / Ribosomal protein L34
Similarity search - Domain/homology
: / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Actinoplanes awajinensis subsp. mycoplanecinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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: Beta sliding clamp
C: Mycoplanecin A
D: Mycoplanecin A


Theoretical massNumber of molelcules
Total (without water)84,2074
Polymers84,2074
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-8 kcal/mol
Surface area33740 Å2
Unit cell
Length a, b, c (Å)83.937, 150.050, 72.381
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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.: 2
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 Mycoplanecin A


Type: Peptide-like / Class: Antimicrobial / Mass: 1201.538 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Actinoplanes awajinensis subsp. mycoplanecinus (bacteria)
References: BIRD: PRD_002467
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAntimycobacterial
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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.2 M CaCl2 0.15 M MgCl2 8.75 % (v/v) Glycerol 17.5 % (w/v) PEG 3350 0.1 M Tris/HCl pH 9.0 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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.27→75.03 Å / Num. obs: 39802 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Χ2: 0.74 / Net I/σ(I): 6.8 / Num. measured all: 280126
Reflection shellResolution: 2.27→2.39 Å / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.66 / Num. measured all: 38813 / Num. unique obs: 5767 / CC1/2: 0.829 / Rpim(I) all: 0.274 / Rrim(I) all: 0.716 / Χ2: 0.56 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
autoPROC1.05data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.201-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→51.28 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 1961 4.93 %
Rwork0.2074 --
obs0.2089 39787 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→51.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 0 70 5854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035948
X-RAY DIFFRACTIONf_angle_d0.5868079
X-RAY DIFFRACTIONf_dihedral_angle_d7.254914
X-RAY DIFFRACTIONf_chiral_restr0.043931
X-RAY DIFFRACTIONf_plane_restr0.0041070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.320.32291310.28132705X-RAY DIFFRACTION99
2.32-2.390.27971390.28312669X-RAY DIFFRACTION99
2.39-2.460.31471470.272637X-RAY DIFFRACTION97
2.46-2.540.35761530.27172681X-RAY DIFFRACTION100
2.54-2.630.31381450.26962725X-RAY DIFFRACTION100
2.63-2.730.30771290.26272699X-RAY DIFFRACTION99
2.73-2.860.3051400.25552729X-RAY DIFFRACTION99
2.86-3.010.30371460.25622699X-RAY DIFFRACTION99
3.01-3.190.28841450.2582718X-RAY DIFFRACTION99
3.19-3.440.27011300.23112665X-RAY DIFFRACTION98
3.44-3.790.25281420.21462704X-RAY DIFFRACTION99
3.79-4.340.18541450.17782721X-RAY DIFFRACTION100
4.34-5.460.16291390.15752739X-RAY DIFFRACTION100
5.46-51.280.23081300.17962735X-RAY DIFFRACTION98
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)
10.6902-0.95450.13562.2060.67621.86140.1903-0.253-0.13470.3561-0.0470.08460.18070.131-00.5623-0.0589-0.06170.65610.07890.5877-21.1776-7.440719.7744
21.0468-0.6684-0.03512.31650.09650.98530.19970.014-0.44070.1685-0.22750.2993-0.00180.16790.00020.5187-0.1042-0.06610.62460.08020.4997-24.3611-4.240419.855
31.93040.0521-0.06220.5216-0.17880.06480.3419-0.0472-0.5439-0.1631-0.1076-0.03420.08850.04830.00010.68-0.0738-0.1370.59180.02560.6179-11.0397-12.226518.3595
43.90761.2088-0.32022.2472-0.30681.44530.36-0.0675-0.3244-0.1416-0.14850.15220.0044-0.1480.00120.5322-0.0317-0.15380.5192-0.03440.62514.1354-14.217917.9274
52.54380.24670.53091.38940.65271.49080.1166-0.0093-0.2441-0.0585-0.0542-0.1581-0.06420.12300.4601-0.05940.00950.5002-0.03750.430927.32360.482417.1968
61.3693-0.67590.42771.57050.7680.90490.5265-0.429-0.28110.03110.11850.09540.1690.68390.00020.4521-0.0857-0.10630.5788-0.08190.472124.5438-6.370918.1908
71.7797-0.99830.16923.1479-0.57481.15550.1711-0.17080.28410.124-0.08210.0202-0.1852-0.10560.00010.6156-0.10340.05350.5573-0.10120.541623.444329.601719.9082
80.4922-0.09120.1080.29240.24440.26930.2286-0.13580.6508-0.1924-0.0593-0.1005-0.07020.1114-00.7554-0.05780.19640.59680.02610.74325.847541.67618.2367
93.24571.8160.04292.45030.27460.53660.1984-0.08140.46020.0463-0.05460.249-0.09-0.1070.00010.5835-0.02810.07140.53230.04340.546-17.462231.064217.6426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 140 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 235 )
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 346 )
6X-RAY DIFFRACTION6chain 'A' and (resid 347 through 366 )
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 365 )

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