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- PDB-7az5: DNA polymerase sliding clamp from Escherichia coli with peptide 4... -

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Basic information

Entry
Database: PDB / ID: 7az5
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 47 bound
Components
  • Beta sliding clamp
  • Peptide 47
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 / molecular replacement / Resolution: 1.87 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Beta sliding clamp
D: Beta sliding clamp
H: Peptide 47
I: Peptide 47
J: Peptide 47
K: Peptide 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,38114
Polymers174,4808
Non-polymers9016
Water18,8621047
1
A: Beta sliding clamp
B: Beta sliding clamp
H: Peptide 47
I: Peptide 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8408
Polymers87,2404
Non-polymers6014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint4 kcal/mol
Surface area33930 Å2
MethodPISA
2
C: Beta sliding clamp
D: Beta sliding clamp
J: Peptide 47
K: Peptide 47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5406
Polymers87,2404
Non-polymers3002
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-5 kcal/mol
Surface area33030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.886, 80.166, 83.371
Angle α, β, γ (deg.)62.790, 71.290, 81.660
Int Tables number1
Space group name H-MP1

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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 (E. coli) / References: UniProt: A0A073FMV0
#2: Protein/peptide
Peptide 47


Mass: 818.013 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1047 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
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: 1.87→65.24 Å / Num. obs: 90577 / % possible obs: 93.5 % / Redundancy: 7 % / Biso Wilson estimate: 26.52 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.135 / Net I/σ(I): 11.1
Reflection shellResolution: 1.87→2.03 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4529 / CC1/2: 0.56 / Rpim(I) all: 0.526

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6fvl


Resolution: 1.87→27.35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.211 4334 4.79 %RANDOM
Rwork0.177 ---
obs0.179 90543 72.8 %-
Displacement parametersBiso max: 130.1 Å2 / Biso mean: 34.66 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0.4205 Å2-0.8615 Å2-0.0624 Å2
2---0.421 Å20.055 Å2
3---0.0005 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.87→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11667 0 90 1085 12842
Biso mean--37.89 40.18 -
Num. residues----1500
LS refinement shellResolution: 1.87→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2604 85 4.69 %
Rwork0.2128 1726 -
all0.2149 1811 -
obs--9.72 %
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)
10.38740.0950.06580.80860.06930.670.0731-0.059-0.08250.1389-0.0567-0.12190.0725-0.03-0.0164-0.0727-0.0168-0.0158-0.00870.03390.06660.4098-0.0655-0.7552
20.40370.1108-0.180.85540.43870.73920.0158-0.00380.0763-0.1471-0.03930.1844-0.0887-0.08630.02350.00760.0045-0.0218-0.0123-0.00350.0463.933531.4314-23.5139
30.5670.2360.11161.26090.10750.2455-0.01180.027-0.0969-0.18410.0176-0.1858-0.03380.093-0.00580.0126-0.00830.02820.0212-0.0307-0.037836.532913.9914-30.5322
40.37420.20930.24231.09440.18210.45080.1282-0.1068-0.05670.2001-0.1047-0.07490.1017-0.0448-0.0235-0.0953-0.0352-0.0041-0.0260.0093-0.0740.335620.35927.6249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 366
2X-RAY DIFFRACTION2{ B|* }B-1 - 366
3X-RAY DIFFRACTION3{ C|* }C-1 - 366
4X-RAY DIFFRACTION4{ D|* }D-1 - 366

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