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

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Basic information

Entry
Database: PDB / ID: 7azk
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 35 bound
Components
  • Beta sliding clamp
  • Peptide 35
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: 2.05 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 / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 35
B: Beta sliding clamp
I: Peptide 35
C: Beta sliding clamp
J: Peptide 35
D: Beta sliding clamp
K: Peptide 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,83025
Polymers174,3428
Non-polymers2,48717
Water17,961997
1
A: Beta sliding clamp
H: Peptide 35
B: Beta sliding clamp
I: Peptide 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,65714
Polymers87,1714
Non-polymers1,48610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-35 kcal/mol
Surface area32570 Å2
MethodPISA
2
C: Beta sliding clamp
J: Peptide 35
D: Beta sliding clamp
K: Peptide 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,17311
Polymers87,1714
Non-polymers1,0027
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-17 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.815, 135.827, 87.541
Angle α, β, γ (deg.)90.000, 106.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 0 and (name N or name...
21(chain B and ((resid 0 and (name N or name...
31(chain C and ((resid 0 and (name N or name...
41(chain D and (resid 0 through 1 or resid 3...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and ((resid 0 and (name N or name...AA020
12SERSERLEULEU(chain A and ((resid 0 and (name N or name...AA-1 - 36619 - 386
13SERSERLEULEU(chain A and ((resid 0 and (name N or name...AA-1 - 36619 - 386
14SERSERLEULEU(chain A and ((resid 0 and (name N or name...AA-1 - 36619 - 386
15SERSERLEULEU(chain A and ((resid 0 and (name N or name...AA-1 - 36619 - 386
21HISHISHISHIS(chain B and ((resid 0 and (name N or name...BC020
22SERSERLEULEU(chain B and ((resid 0 and (name N or name...BC-1 - 36619 - 386
23SERSERLEULEU(chain B and ((resid 0 and (name N or name...BC-1 - 36619 - 386
24SERSERLEULEU(chain B and ((resid 0 and (name N or name...BC-1 - 36619 - 386
25SERSERLEULEU(chain B and ((resid 0 and (name N or name...BC-1 - 36619 - 386
31HISHISHISHIS(chain C and ((resid 0 and (name N or name...CE020
32SERSERLEULEU(chain C and ((resid 0 and (name N or name...CE-1 - 36619 - 386
33SERSERLEULEU(chain C and ((resid 0 and (name N or name...CE-1 - 36619 - 386
34SERSERLEULEU(chain C and ((resid 0 and (name N or name...CE-1 - 36619 - 386
35SERSERLEULEU(chain C and ((resid 0 and (name N or name...CE-1 - 36619 - 386
41HISHISMETMET(chain D and (resid 0 through 1 or resid 3...DG0 - 120 - 21
42PHEPHETHRTHR(chain D and (resid 0 through 1 or resid 3...DG3 - 423 - 24
43GLUGLUALAALA(chain D and (resid 0 through 1 or resid 3...DG6 - 5526 - 75
44VALVALPROPRO(chain D and (resid 0 through 1 or resid 3...DG57 - 11777 - 137
45GLUGLUGLYGLY(chain D and (resid 0 through 1 or resid 3...DG166 - 19186 - 39
46LYSLYSLEULEU(chain D and (resid 0 through 1 or resid 3...DG198 - 203218 - 223
47METMETGLYGLY(chain D and (resid 0 through 1 or resid 3...DG206 - 210226 - 230
48ASPASPASPASP(chain D and (resid 0 through 1 or resid 3...DG211231
49HISHISLEULEU(chain D and (resid 0 through 1 or resid 3...DG0 - 36620 - 386
410HISHISLEULEU(chain D and (resid 0 through 1 or resid 3...DG0 - 36620 - 386
411HISHISLEULEU(chain D and (resid 0 through 1 or resid 3...DG0 - 36620 - 386
412HISHISLEULEU(chain D and (resid 0 through 1 or resid 3...DG0 - 36620 - 386

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDHIJK

#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 35


Mass: 783.739 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 1014 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 997 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Potassium thiocyanate, 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-F / 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: 2.05→135.82 Å / Num. obs: 87312 / % possible obs: 94.1 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rpim(I) all: 0.061 / Net I/σ(I): 10.2
Reflection shellResolution: 2.05→2.08 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 180 / CC1/2: 0.43 / Rpim(I) all: 0.572

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FVL

6fvl


Resolution: 2.05→84.09 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 4327 4.96 %
Rwork0.2097 82965 -
obs0.2112 87292 78.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.65 Å2 / Biso mean: 36.2021 Å2 / Biso min: 16.04 Å2
Refinement stepCycle: final / Resolution: 2.05→84.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11542 0 339 1018 12899
Biso mean--47.59 41.53 -
Num. residues----1462
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6706X-RAY DIFFRACTION12.02TORSIONAL
12B6706X-RAY DIFFRACTION12.02TORSIONAL
13C6706X-RAY DIFFRACTION12.02TORSIONAL
14D6706X-RAY DIFFRACTION12.02TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.265810.352228291
2.08-2.10.3314220.255538240411
2.1-2.130.3365460.270578382923
2.13-2.150.2692590.28581258131735
2.15-2.180.2894740.26971488156242
2.18-2.210.2969880.26441755184350
2.21-2.240.3142970.27011946204355
2.24-2.280.2891020.27791578168045
2.28-2.310.29171310.25522406253769
2.31-2.350.26741170.26952672278974
2.35-2.390.26931570.27052720287779
2.39-2.440.27851590.25512987314684
2.44-2.480.29361690.25053123329289
2.48-2.530.29441670.24893310347795
2.53-2.590.2891870.24533484367198
2.59-2.650.33261680.243835403708100
2.65-2.710.32781960.234734643660100
2.71-2.790.23071940.227335153709100
2.79-2.870.28692080.223634983706100
2.87-2.960.25991710.218635533724100
2.96-3.070.24981830.211835253708100
3.07-3.190.25091950.215235103705100
3.19-3.340.23051920.206735243716100
3.34-3.510.23431820.188935353717100
3.51-3.730.21361660.1835553721100
3.73-4.020.19211760.171635553731100
4.02-4.420.1991790.165435503729100
4.43-5.060.16541900.151735423732100
5.07-6.380.23441700.225435773747100
6.38-84.090.25771810.23833602378399
Refinement TLS params.Method: refined / Origin x: 41.9957 Å / Origin y: -9.3861 Å / Origin z: 41.7378 Å
111213212223313233
T0.2078 Å20.0115 Å20.0001 Å2-0.2085 Å20.0129 Å2--0.2051 Å2
L0.1561 °20.0249 °20.046 °2-0.2153 °20.1189 °2--0.1108 °2
S-0.0115 Å °-0.0119 Å °-0.0017 Å °0.0525 Å °0.0092 Å °-0.0451 Å °0.0362 Å °0.0255 Å °0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 366
2X-RAY DIFFRACTION1allH367 - 368
3X-RAY DIFFRACTION1allH369 - 371
4X-RAY DIFFRACTION1allH372
5X-RAY DIFFRACTION1allA401
6X-RAY DIFFRACTION1allB-1 - 366
7X-RAY DIFFRACTION1allI367 - 368
8X-RAY DIFFRACTION1allI369 - 371
9X-RAY DIFFRACTION1allI372
10X-RAY DIFFRACTION1allC-1 - 366
11X-RAY DIFFRACTION1allJ367 - 368
12X-RAY DIFFRACTION1allJ369 - 371
13X-RAY DIFFRACTION1allJ372
14X-RAY DIFFRACTION1allC401 - 501
15X-RAY DIFFRACTION1allD0 - 366
16X-RAY DIFFRACTION1allK367 - 368
17X-RAY DIFFRACTION1allK369 - 371
18X-RAY DIFFRACTION1allK372
19X-RAY DIFFRACTION1allD401
20X-RAY DIFFRACTION1allE1 - 2
21X-RAY DIFFRACTION1allF1 - 11
22X-RAY DIFFRACTION1allG1 - 3
23X-RAY DIFFRACTION1allW1 - 1258

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