[English] 日本語
Yorodumi
- PDB-7azg: DNA polymerase sliding clamp from Escherichia coli with peptide 4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7azg
TitleDNA polymerase sliding clamp from Escherichia coli with peptide 4 bound
Components
  • Beta sliding clamp
  • Peptide 4
KeywordsDNA BINDING PROTEIN / antibacterial drug
Function / homologyDNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / :
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: 2.92 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
Item: _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
C: Beta sliding clamp
D: Beta sliding clamp
E: Beta sliding clamp
F: Beta sliding clamp
G: Beta sliding clamp
H: Beta sliding clamp
I: Peptide 4
J: Peptide 4
K: Peptide 4
L: Peptide 4
M: Peptide 4
N: Peptide 4
O: Peptide 4
P: Peptide 4


Theoretical massNumber of molelcules
Total (without water)348,38216
Polymers348,38216
Non-polymers00
Water9,080504
1
A: Beta sliding clamp
B: Beta sliding clamp
I: Peptide 4
J: Peptide 4


Theoretical massNumber of molelcules
Total (without water)87,0954
Polymers87,0954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-21 kcal/mol
Surface area32900 Å2
MethodPISA
2
C: Beta sliding clamp
D: Beta sliding clamp
K: Peptide 4
L: Peptide 4


Theoretical massNumber of molelcules
Total (without water)87,0954
Polymers87,0954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-20 kcal/mol
Surface area32800 Å2
MethodPISA
3
E: Beta sliding clamp
F: Beta sliding clamp
M: Peptide 4
N: Peptide 4


Theoretical massNumber of molelcules
Total (without water)87,0954
Polymers87,0954
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-22 kcal/mol
Surface area32990 Å2
MethodPISA
4
G: Beta sliding clamp
H: Beta sliding clamp
O: Peptide 4
P: Peptide 4


Theoretical massNumber of molelcules
Total (without water)87,0954
Polymers87,0954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-17 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.422, 165.302, 138.510
Angle α, β, γ (deg.)90.000, 91.840, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Beta sliding clamp


Mass: 42801.863 Da / Num. of mol.: 8
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: Protein/peptide
Peptide 4


Mass: 745.863 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.2 M Succinic acid pH 7.0, PEG 3350 20% (w/v)

-
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: 2.92→33.65 Å / Num. obs: 46885 / % possible obs: 93.2 % / Redundancy: 7 % / Biso Wilson estimate: 66.05 Å2 / CC1/2: 0.98 / Rsym value: 0.17 / Net I/σ(I): 6.4
Reflection shellResolution: 2.92→3.22 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2342 / CC1/2: 0.39 / Rpim(I) all: 0.814

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

6fvl


Resolution: 2.92→33.65 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.843 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.531
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2290 4.88 %RANDOM
Rwork0.184 ---
obs0.187 46885 68.6 %-
Displacement parametersBiso max: 194.73 Å2 / Biso mean: 66.18 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-3.6525 Å20 Å20.5787 Å2
2---3.9608 Å20 Å2
3---0.3083 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: final / Resolution: 2.92→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23067 0 416 505 23988
Biso mean--49.07 21.6 -
Num. residues----2936
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8390SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4069HARMONIC5
X-RAY DIFFRACTIONt_it23562HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3050SEMIHARMONIC5
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_contact25784SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d23562HARMONIC40.007
X-RAY DIFFRACTIONt_angle_deg31926HARMONIC40.86
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion17.27
LS refinement shellResolution: 2.92→3.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2032 47 5.01 %
Rwork0.2105 891 -
all0.2102 938 -
obs--8.01 %
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)
10.607-0.2242-0.10442.5785-0.9021.4227-0.0347-0.08140.01920.2280.05780.518-0.1055-0.2469-0.0232-0.21320.02140.1095-0.13230.00370.06727.3969-0.600111.3865
20.64780.04860.47121.9755-0.31331.1079-0.0270.05040.0466-0.1540.04780.30590.0594-0.1202-0.0208-0.1361-0.0928-0.0313-0.1387-0.05360.038226.2244-29.7715-13.7616
31.0880.27130.29851.36140.82242.3025-0.05010.0928-0.0196-0.1990.104-0.2749-0.24070.0575-0.0538-0.1833-0.09510.1221-0.21440.05990.103759.75653.347-6.3921
40.73940.08270.4431.88811.2692.1048-0.06440.0328-0.22160.27470.2244-0.24630.46790.419-0.16-0.17180.11830.015-0.1833-0.08330.132764.6674-30.571611.3635
50.9495-0.75230.11712.15281.60392.39330.2005-0.1634-0.2880.04920.0012-0.12630.09580.0491-0.2017-0.1382-0.0178-0.1512-0.21540.08860.079675.31-68.8178.351
61.00840.00690.41071.4385-0.04871.6110.08320.26080.2425-0.1118-0.1027-0.3267-0.1640.19330.0195-0.1260.05880.1465-0.13740.1232-0.045879.6015-37.158256.3731
71.43440.1733-0.00441.351-0.63161.37010.20370.3404-0.5471-0.1654-0.23580.52030.1702-0.37860.032-0.22620.0156-0.1204-0.2312-0.21910.207242.9241-67.709659.857
81.3201-0.50760.26452.5262-0.53811.14750.0616-0.24860.25150.1267-0.11360.3001-0.244-0.27610.052-0.27810.01590.2051-0.1386-0.18630.030940.8172-35.541581.3398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 366
2X-RAY DIFFRACTION2{ B|* }B-1 - 366
3X-RAY DIFFRACTION3{ C|* }C-1 - 366
4X-RAY DIFFRACTION4{ D|* }D-1 - 366
5X-RAY DIFFRACTION5{ E|* }E-1 - 366
6X-RAY DIFFRACTION6{ F|* }F0 - 366
7X-RAY DIFFRACTION7{ G|* }G0 - 366
8X-RAY DIFFRACTION8{ H|* }H-1 - 366

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more