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

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Basic information

Entry
Database: PDB / ID: 8ciy
TitleDNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Cyclohexyl-Griselimycin.
Components
  • Beta sliding clamp
  • Cyclohexyl-Griselimycin
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
: / ACETATE ION / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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: Cyclohexyl-Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,72817
Polymers42,0992
Non-polymers62815
Water7,368409
1
A: Beta sliding clamp
B: Cyclohexyl-Griselimycin
hetero molecules

A: Beta sliding clamp
B: Cyclohexyl-Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,45534
Polymers84,1994
Non-polymers1,25630
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area9090 Å2
ΔGint-215 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.907, 150.723, 71.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-825-

HOH

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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 Cyclohexyl-Griselimycin


Type: Peptide-like / Class: Antibiotic / Mass: 1197.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002466

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Non-polymers , 6 types, 424 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsNovel synthetic analog of natural product Griselimycin
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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.64 M CaCl2 0.5 M Li Acetate 9.4 % (w/v) PEG 8000 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: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→19.98 Å / Num. obs: 67324 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Χ2: 0.88 / Net I/σ(I): 21.4 / Num. measured all: 901633
Reflection shellResolution: 1.54→1.62 Å / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.918 / Num. measured all: 123025 / Num. unique obs: 9751 / CC1/2: 0.876 / Rpim(I) all: 0.268 / Rrim(I) all: 0.957 / Χ2: 0.73 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROC1.0.5data processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→19.98 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 3527 5.24 %
Rwork0.1709 --
obs0.1724 67313 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 113 409 3289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073201
X-RAY DIFFRACTIONf_angle_d0.9964381
X-RAY DIFFRACTIONf_dihedral_angle_d14.5881272
X-RAY DIFFRACTIONf_chiral_restr0.055499
X-RAY DIFFRACTIONf_plane_restr0.011586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.26161370.23832507X-RAY DIFFRACTION100
1.56-1.580.29741230.23592547X-RAY DIFFRACTION100
1.58-1.610.28771170.22572543X-RAY DIFFRACTION100
1.61-1.630.23931500.21762527X-RAY DIFFRACTION100
1.63-1.660.23681490.20882513X-RAY DIFFRACTION100
1.66-1.690.25221560.2022506X-RAY DIFFRACTION100
1.69-1.720.23391320.20092529X-RAY DIFFRACTION100
1.72-1.750.22351590.18362529X-RAY DIFFRACTION100
1.75-1.790.21941330.18262524X-RAY DIFFRACTION100
1.79-1.820.22421540.18142502X-RAY DIFFRACTION100
1.82-1.870.23641420.17182561X-RAY DIFFRACTION100
1.87-1.910.191530.17422483X-RAY DIFFRACTION100
1.91-1.970.16631090.16542613X-RAY DIFFRACTION100
1.97-2.020.21811450.16042500X-RAY DIFFRACTION100
2.02-2.090.20311730.1632504X-RAY DIFFRACTION100
2.09-2.160.17381300.15792586X-RAY DIFFRACTION100
2.16-2.250.18481390.15322537X-RAY DIFFRACTION100
2.25-2.350.18421440.16392539X-RAY DIFFRACTION100
2.35-2.480.20811470.1652562X-RAY DIFFRACTION100
2.48-2.630.18081750.17332535X-RAY DIFFRACTION100
2.63-2.830.20431460.17142543X-RAY DIFFRACTION100
2.83-3.120.20161320.1692614X-RAY DIFFRACTION100
3.12-3.570.17991460.16342583X-RAY DIFFRACTION100
3.57-4.480.16881330.14612632X-RAY DIFFRACTION100
4.48-19.980.23371030.18712767X-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)
11.0598-0.5049-0.23811.07860.36181.42570.00770.0113-0.09810.04440.0162-0.00780.07560.1221-0.02350.13230.0051-0.00750.13850.00130.1377-65.5375-16.465720.3437
22.8474-0.12180.14870.08490.07890.0928-0.0509-0.101-0.2742-0.00480.02660.04890.0313-0.05350.01770.20080.0088-0.01560.1831-0.01410.2135-39.3638-27.060317.6376
30.92960.39220.291.07370.40710.56360.03920.0334-0.1377-0.045-0.0288-0.02450.044-0.0078-0.01060.140.0101-0.00630.1567-0.01670.1549-14.9814-13.332917.529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 235 )
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 366 )

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