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- PDB-7azl: DNA polymerase sliding clamp from Escherichia coli with peptide 3... -

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Basic information

Entry
Database: PDB / ID: 7azl
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 38 bound
Components
  • Beta sliding clamp
  • Peptide 38
KeywordsDNA BINDING PROTEIN / antibacterial drug
Function / homologyDNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli 2-427-07_S4_C3 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMonsarrat, C. / Compain, G. / Andre, C. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Brillet, K. / Landolfo, M. / Silva da Veiga, C. ...Monsarrat, C. / Compain, G. / Andre, C. / Martiel, I. / Engilberge, S. / Olieric, V. / Wolff, P. / Brillet, K. / Landolfo, M. / Silva da Veiga, C. / Wagner, J. / Guichard, G. / Burnouf, D.Y.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp.
Authors: Monsarrat, C. / Compain, G. / Andre, C. / Engilberge, S. / Martiel, I. / Olieric, V. / Wolff, P. / Brillet, K. / Landolfo, M. / Silva da Veiga, C. / Wagner, J. / Guichard, G. / Burnouf, D.Y.
History
DepositionNov 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
C: Beta sliding clamp
D: Beta sliding clamp
E: Peptide 38
G: Peptide 38
F: Peptide 38
H: Peptide 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,07511
Polymers174,7718
Non-polymers3043
Water7,512417
1
A: Beta sliding clamp
D: Beta sliding clamp
E: Peptide 38
H: Peptide 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5846
Polymers87,3854
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-10 kcal/mol
Surface area33160 Å2
MethodPISA and gel filtration
2
B: Beta sliding clamp
C: Beta sliding clamp
G: Peptide 38
F: Peptide 38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4925
Polymers87,3854
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-8 kcal/mol
Surface area32840 Å2
MethodPISA and gel filtration
Unit cell
Length a, b, c (Å)139.611, 86.643, 153.897
Angle α, β, γ (deg.)90.000, 92.560, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Beta sliding clamp


Mass: 42801.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2-427-07_S4_C3 (bacteria)
Gene: dnaN, AD31_4438 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A073FMV0
#2: Protein/peptide
Peptide 38


Mass: 890.849 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.2 M Sodium formate pH 7.2, PEG 3350 20% (w/v)

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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 / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→70.69 Å / Num. obs: 70023 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rpim(I) all: 0.051 / Net I/σ(I): 11.3
Reflection shellResolution: 2.42→2.46 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3408 / CC1/2: 0.72 / Rpim(I) all: 0.39

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FVL

6fvl


Resolution: 2.42→70.69 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 --
Rwork0.208 --
obs0.21 70023 99.9 %
Displacement parametersBiso mean: 49.63 Å2
Refinement stepCycle: LAST / Resolution: 2.42→70.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11136 0 264 417 11817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011711610
X-RAY DIFFRACTIONf_angle_d1.527315682
X-RAY DIFFRACTIONf_chiral_restr0.08921808
X-RAY DIFFRACTIONf_plane_restr0.0072077
X-RAY DIFFRACTIONf_dihedral_angle_d21.87274406

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