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- PDB-7azd: DNA polymerase sliding clamp from Escherichia coli with peptide 2... -

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Basic information

Entry
Database: PDB / ID: 7azd
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 20 bound
Components
  • Beta sliding clamp
  • Peptide 20
KeywordsDNA BINDING PROTEIN / antibacterial drug
Function / homologyDI(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: 2.19 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_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_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.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_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.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / 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
B: Beta sliding clamp
C: Beta sliding clamp
D: Beta sliding clamp
H: Peptide 20
I: Peptide 20
J: Peptide 20
K: Peptide 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,31013
Polymers174,5158
Non-polymers7955
Water12,160675
1
A: Beta sliding clamp
D: Beta sliding clamp
H: Peptide 20
K: Peptide 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6026
Polymers87,2584
Non-polymers3442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-14 kcal/mol
Surface area32670 Å2
MethodPISA
2
B: Beta sliding clamp
C: Beta sliding clamp
I: Peptide 20
J: Peptide 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7087
Polymers87,2584
Non-polymers4513
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-3 kcal/mol
Surface area32790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.677, 81.757, 141.926
Angle α, β, γ (deg.)90.000, 97.490, 90.000
Int Tables number4
Space group name H-MP1211

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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 20


Mass: 826.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / 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.: 675 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1M Sodium malonate pH5.0, PEG 3350 12% (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: 2.19→70.69 Å / Num. obs: 58310 / % possible obs: 94 % / Redundancy: 13.7 % / Biso Wilson estimate: 44.37 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.044 / Net I/σ(I): 13.1
Reflection shellResolution: 2.19→2.44 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2915 / CC1/2: 0.578 / Rpim(I) all: 0.524

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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: 2.19→41.39 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.907 / SU R Cruickshank DPI: 0.543 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.569 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.272
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2845 4.88 %RANDOM
Rwork0.189 ---
obs0.191 58300 71.7 %-
Displacement parametersBiso max: 153.78 Å2 / Biso mean: 51.4 Å2 / Biso min: 7.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.121 Å20 Å2-0.2918 Å2
2---0.4521 Å20 Å2
3----0.6689 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.19→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11472 0 132 677 12281
Biso mean--38.32 45.42 -
Num. residues----1479
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4243SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2037HARMONIC5
X-RAY DIFFRACTIONt_it11886HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1527SEMIHARMONIC5
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_contact13637SEMIHARMONIC3
X-RAY DIFFRACTIONt_bond_d11886HARMONIC30.011
X-RAY DIFFRACTIONt_angle_deg16078HARMONIC31.09
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion17.59
LS refinement shellResolution: 2.19→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2503 62 5.32 %
Rwork0.2215 1104 -
all0.2231 1166 -
obs--7.4 %
Refinement TLS params.Method: refined / Origin x: -2.8907 Å / Origin y: 19.6284 Å / Origin z: 36.0182 Å
111213212223313233
T0.1555 Å20.0166 Å2-0.0022 Å2-0.1644 Å2-0.0006 Å2--0.0935 Å2
L0.5352 °20.1315 °20.4557 °2-0.0043 °20.5003 °2--0.8513 °2
S-0.0311 Å °0.2598 Å °0.008 Å °0.0246 Å °0.1041 Å °-0.0006 Å °-0.1283 Å °-0.0397 Å °-0.0731 Å °
Refinement TLS groupSelection details: { K|* }

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