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- PDB-7aze: DNA polymerase sliding clamp from Escherichia coli with peptide 1... -

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Basic information

Entry
Database: PDB / ID: 7aze
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 18 bound
Components
  • Beta sliding clamp
  • Peptide 18
KeywordsDNA BINDING PROTEIN / antibacterial drug
Function / homologyDNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / MALONATE ION / :
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: 1.82 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 2.0Jun 21, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
H: Peptide 18
I: Peptide 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,25110
Polymers87,2504
Non-polymers1,0016
Water13,331740
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-11 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 64.810, 71.100
Angle α, β, γ (deg.)106.710, 100.070, 116.950
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABHI

#1: Protein Beta sliding clamp


Mass: 42801.863 Da / Num. of mol.: 2
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 18


Mass: 822.919 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 746 molecules

#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 8% v/v Tacsimate pH 6.0, 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: 1.82→53.86 Å / Num. obs: 60806 / % possible obs: 90.3 % / Redundancy: 6 % / Biso Wilson estimate: 24.07 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.091 / Net I/σ(I): 8.5
Reflection shellResolution: 1.82→1.99 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3041 / CC1/2: 0.844 / Rpim(I) all: 1.154

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6fvl


Resolution: 1.82→52.87 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3008 4.95 %RANDOM
Rwork0.193 ---
obs0.195 60806 74.5 %-
Displacement parametersBiso max: 104.9 Å2 / Biso mean: 28.95 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.0894 Å20.1354 Å2-0.5132 Å2
2--0.3607 Å2-1.1207 Å2
3----0.2712 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.82→52.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 126 759 6633
Biso mean--32.43 40 -
Num. residues----740
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2202SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1053HARMONIC5
X-RAY DIFFRACTIONt_it6083HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion771SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7442SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6083HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8260HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion17.16
LS refinement shellResolution: 1.82→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2909 62 5.09 %
Rwork0.2474 1155 -
all0.2496 1217 -
obs--8.48 %
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)
10.4015-0.22040.03990.41830.0220.7845-0.0014-0.05270.00980.01580.0533-0.0260.10080.109-0.0519-0.0356-0.0302-0.0216-0.0492-0.01720.0226-0.05760.3839-0.4758
20.458-0.1479-0.27640.1020.07780.98720.02510.06660.01480.0077-0.0085-0.01850.0072-0.1678-0.0166-0.0059-0.0233-0.0124-0.0282-0.00750.0149-29.148117.9308-19.1713
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

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