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- PDB-7az6: DNA polymerase sliding clamp from Escherichia coli with peptide 3... -

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Basic information

Entry
Database: PDB / ID: 7az6
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 36 bound
Components
  • Beta sliding clamp
  • Peptide 36
KeywordsDNA BINDING PROTEIN / antibacterial drug
Function / homologyDNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / ACETATE ION / 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 / molecular replacement / Resolution: 1.93 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sliding clamp
H: Peptide 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1427
Polymers43,7432
Non-polymers3995
Water7,656425
1
A: Beta sliding clamp
H: Peptide 36
hetero molecules

A: Beta sliding clamp
H: Peptide 36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,28314
Polymers87,4864
Non-polymers79810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area7790 Å2
ΔGint-22 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.289, 66.451, 80.272
Angle α, β, γ (deg.)90.000, 127.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-942-

HOH

21A-1107-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AH

#1: Protein Beta sliding clamp


Mass: 42801.863 Da / Num. of mol.: 1
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 (E. coli) / References: UniProt: A0A073FMV0
#2: Protein/peptide Peptide 36


Mass: 940.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 430 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 2% v/v Tacsimate pH 5, 0.1M Sodium citrate tribasic dihydrate pH5.6, PEG 3350 16% (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, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→53.9 Å / Num. obs: 32437 / % possible obs: 95.8 % / Redundancy: 11 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.07 / Net I/σ(I): 8.5
Reflection shellResolution: 1.93→1.96 Å / Num. unique obs: 888 / CC1/2: 0.7 / Rpim(I) all: 0.42

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER3.2.8refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FVL

6fvl


Resolution: 1.93→52.47 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.188 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.154
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1509 4.66 %RANDOM
Rwork0.205 ---
obs0.207 32390 95.7 %-
Displacement parametersBiso max: 102.38 Å2 / Biso mean: 34.19 Å2 / Biso min: 21.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.6937 Å20 Å2-4.4798 Å2
2--0.1085 Å20 Å2
3----0.8021 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.93→52.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 23 437 3377
Biso mean--27.44 47.66 -
Num. residues----375
LS refinement shellResolution: 1.93→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3001 27 4.17 %
Rwork0.2448 621 -
all0.2472 648 -
obs--44.36 %
Refinement TLS params.Method: refined / Origin x: 12.5324 Å / Origin y: 0.5956 Å / Origin z: 22.897 Å
111213212223313233
T0.3702 Å2-0.0029 Å2-0.2542 Å2-0.0829 Å2-0.0045 Å2--0.2528 Å2
L0.4133 °20.0456 °20.0331 °2-0.0351 °20.024 °2--0.3641 °2
S0.0189 Å °0.0614 Å °-0.0339 Å °0.026 Å °0.0076 Å °-0.0235 Å °0.0376 Å °-0.111 Å °-0.0264 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A-1 - 366
2X-RAY DIFFRACTION1{ *|* }A-1 - 366
3X-RAY DIFFRACTION1{ *|* }B-1 - 366
4X-RAY DIFFRACTION1{ *|* }H-1 - 366
5X-RAY DIFFRACTION1{ *|* }W-1 - 366

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