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- PDB-7az7: DNA polymerase sliding clamp from Escherichia coli with peptide 3... -

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Basic information

Entry
Database: PDB / ID: 7az7
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 37 bound
Components
  • Beta sliding clamp
  • Peptide 37
KeywordsDNA BINDING PROTEIN / antibacterial drug
Function / homologyDNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / FORMIC ACID / polypeptide(D) / :
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: 1.65 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
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

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
H: Peptide 37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0424
Polymers43,7582
Non-polymers2842
Water8,791488
1
A: Beta sliding clamp
H: Peptide 37
hetero molecules

A: Beta sliding clamp
H: Peptide 37
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0848
Polymers87,5164
Non-polymers5694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6410 Å2
ΔGint-12 kcal/mol
Surface area33530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.180, 67.620, 81.520
Angle α, β, γ (deg.)90.000, 128.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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 BL21(DE3) (bacteria) / References: UniProt: A0A073FMV0
#2: Polypeptide(D) Peptide 37


Mass: 955.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.2 M Ammonium formate, pH 6.6, 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, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→53.99 Å / Num. obs: 39718 / % possible obs: 86.7 % / Redundancy: 13 % / Biso Wilson estimate: 27.22 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.027 / Net I/σ(I): 14.5
Reflection shellResolution: 1.64→1.67 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 61 / CC1/2: 0.18 / Rpim(I) all: 0.68

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FVL

6fvl


Resolution: 1.65→53.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2082 5.24 %RANDOM
Rwork0.184 ---
obs0.186 39717 71.6 %-
Displacement parametersBiso max: 119.39 Å2 / Biso mean: 31.41 Å2 / Biso min: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.1539 Å20 Å2-0.0174 Å2
2--0.4639 Å20 Å2
3----0.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.65→53.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 35 508 3451
Biso mean--21.29 44.93 -
Num. residues----372
LS refinement shellResolution: 1.65→1.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2187 40 5.03 %
Rwork0.225 755 -
all0.2247 795 -
obs--10.86 %

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