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- PDB-7azf: DNA polymerase sliding clamp from Escherichia coli with peptide 8... -

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Basic information

Entry
Database: PDB / ID: 7azf
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 8 bound
Components
  • Beta sliding clamp
  • Peptide 8
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: 1.93 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
Revision 2.0Jun 21, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / 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.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.pdbx_auth_asym_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_alt_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 / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_ref_seq.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 16, 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
C: Beta sliding clamp
D: Beta sliding clamp
H: Peptide 8
I: Peptide 8
J: Peptide 8
K: Peptide 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,14110
Polymers166,9438
Non-polymers1982
Water19,1141061
1
A: Beta sliding clamp
B: Beta sliding clamp
H: Peptide 8
I: Peptide 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6706
Polymers83,4714
Non-polymers1982
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-13 kcal/mol
Surface area33500 Å2
2
C: Beta sliding clamp
D: Beta sliding clamp
J: Peptide 8
K: Peptide 8


Theoretical massNumber of molelcules
Total (without water)83,4714
Polymers83,4714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-13 kcal/mol
Surface area33850 Å2
Unit cell
Length a, b, c (Å)70.418, 82.034, 82.392
Angle α, β, γ (deg.)116.870, 100.260, 95.470
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta sliding clamp


Mass: 40912.781 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 8


Mass: 822.947 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1061 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.2 M DL Malic acid pH 7.0, 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: 1.92→71.7 Å / Num. obs: 84971 / % possible obs: 87.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.24 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.079 / Net I/σ(I): 8.8
Reflection shellResolution: 1.92→1.95 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 99 / CC1/2: 0.38 / Rpim(I) all: 0.727

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6fvl


Resolution: 1.93→37.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4135 4.87 %RANDOM
Rwork0.204 ---
obs0.206 84960 70.8 %-
Displacement parametersBiso max: 166.25 Å2 / Biso mean: 53.43 Å2 / Biso min: 7.12 Å2
Baniso -1Baniso -2Baniso -3
1-3.6832 Å2-1.2059 Å2-1.9506 Å2
2---0.7077 Å22.5963 Å2
3----2.9754 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.93→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11541 0 88 1084 12713
Biso mean--45.21 49.05 -
Num. residues----1490
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5306SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3836HARMONIC5
X-RAY DIFFRACTIONt_it23752HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1539SEMIHARMONIC5
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_contact25710SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d23752HARMONIC40.01
X-RAY DIFFRACTIONt_angle_deg43026HARMONIC40.94
X-RAY DIFFRACTIONt_omega_torsion4.31
X-RAY DIFFRACTIONt_other_torsion15.49
LS refinement shellResolution: 1.93→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2892 94 5.53 %
Rwork0.255 1606 -
all0.2569 1700 -
obs--12.61 %
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)
10.13270.0765-0.35310.3802-0.4290.79140.0077-0.07760.0516-0.193900.04150.26840.1395-0.00770.08070.0324-0.06-0.03420.0407-0.0951-12.272945.488-12.8421
20.05280.0952-0.21370.6705-0.56690.91810.11130.028-0.03810.2261-0.1481-0.0626-0.29590.18190.03690.0437-0.1195-0.01220.01410.0223-0.1345-8.127181.2578-0.4767
30.47530.28490.69720.9486-0.70430.69350.1252-0.0773-0.13890.29310.21170.3282-0.4028-0.1752-0.3369-0.12380.13170.2048-0.13460.13840.1239-46.103775.16337.0983
40.4974-0.2490.6210.6752-0.02561.07860.31150.0239-0.1344-0.42620.01730.30680.09190.1193-0.3288-0.04350.0442-0.3696-0.25470.01470.0788-43.531562.783-29.0139
50.19240.04420.2581-0.09460.21360.72880.00340.0041-0.00150.00310.00310.0022-0.00460.0027-0.00650.1237-0.0022-0.0933-0.0520.0668-0.0389-21.922950.3168-35.0418
60.2029-0.1797-0.36340.01450.09550.2160.0029-0.0030.001-0.00220.00050.0005-0.0057-0.0115-0.00340.0801-0.02110.0737-0.0920.0194-0.0118-24.462279.612718.9408
70.08450.20960.00640.31850.0253-0.0242-0.0058-0.00860.00650.00460.0081-0.00580.00090.001-0.00220.0163-0.03520.0571-0.01310.01-0.0127-29.861693.29555.5307
80.0722-0.2381-0.06430.35560.03330.025-0.00050.0005-0.00940.00210.00120.00210.0025-0.0007-0.00070.05710.0768-0.1172-0.08370.03780.0032-34.401740.1049-24.2865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-2 - 366
2X-RAY DIFFRACTION2{ B|* }B-2 - 366
3X-RAY DIFFRACTION3{ C|* }C-1 - 366
4X-RAY DIFFRACTION4{ D|* }D-1 - 366
5X-RAY DIFFRACTION5{ H|* }H1 - 2
6X-RAY DIFFRACTION6{ I|* }I1 - 2
7X-RAY DIFFRACTION7{ J|* }J1 - 2
8X-RAY DIFFRACTION8{ K|* }K1 - 2

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