[English] 日本語
Yorodumi
- PDB-6pth: Crystal structure of a DnaN sliding clamp (DNA polymerase III sub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pth
TitleCrystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Pseudomonas aeruginosa bound to griselimycin
Components
  • Beta sliding clamp
  • Griselimycin
KeywordsTRANSFERASE/ANTIBIOTIC / NIAID / structural genomics / natural product / broad spectrum / antibiotic / Seattle Structural Genomics Center for Infectious Disease / SSGCID / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / :
Similarity search - Domain/homology
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / Beta sliding clamp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Streptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Pseudomonas aeruginosa bound to griselimycin
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta sliding clamp
G: Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0553
Polymers52,9592
Non-polymers961
Water1629
1
A: Beta sliding clamp
G: Griselimycin
hetero molecules

A: Beta sliding clamp
G: Griselimycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1116
Polymers105,9194
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area5720 Å2
ΔGint-59 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.650, 139.650, 173.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Beta sliding clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / ...Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / DNA polymerase III subunit beta


Mass: 51843.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dnaN, PA0002 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I7C4
#2: Protein/peptide Griselimycin / ACE-MVA-MP8-NCZ-LEU-MP8-LEU-MVA-PRO-MLU-GLY


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces griseus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.59 Å3/Da / Density % sol: 73.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PsaeA.17987.a.EN11.PD38369 at 20.74 mg/mL with 0.8 mM griselimycin against MCSG screen condition A5 optimization screening 0.1 M sodium acetate pH 4.2, 1.4 M ammonium sulfate, 0.2 M sodium ...Details: PsaeA.17987.a.EN11.PD38369 at 20.74 mg/mL with 0.8 mM griselimycin against MCSG screen condition A5 optimization screening 0.1 M sodium acetate pH 4.2, 1.4 M ammonium sulfate, 0.2 M sodium chloride, supplemented with 25% ethylene glycol as cryo-protectant; crystal tracking ID 310486b9, unique puck ID bbz4-5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.05→45.711 Å / Num. obs: 19666 / % possible obs: 99.8 % / Redundancy: 8.031 % / Biso Wilson estimate: 82.516 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 1.042 / Net I/σ(I): 21.4 / Num. measured all: 157945
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.05-3.138.3340.6082.8711792141414150.8920.648100
3.13-3.228.30.463.8911437137813780.9190.49100
3.22-3.318.3360.3644.911270135213520.9510.387100
3.31-3.418.260.2517.1410788130713060.980.26899.9
3.41-3.528.3240.1899.610621127612760.9870.201100
3.52-3.658.2650.15511.6710174123312310.9910.16599.8
3.65-3.788.1890.11515.889884120712070.9930.123100
3.78-3.948.1950.09219.39252112911290.9970.098100
3.94-4.118.0820.07922.619125112911290.9970.085100
4.11-4.318.0970.06427.548518105210520.9980.068100
4.31-4.557.9970.0533.428085101210110.9980.05399.9
4.55-4.827.840.04635.5776059729700.9990.04999.8
4.82-5.167.8960.04834.9771709089080.9990.052100
5.16-5.577.9410.04934.6868218598590.9980.052100
5.57-6.17.7840.04634.4261187867860.9990.049100
6.1-6.827.7750.0438.0256067217210.9990.043100
6.82-7.887.5630.03244.4949546556550.9990.035100
7.88-9.657.2890.02747.8840825615600.9990.02999.8
9.65-13.646.8480.02547.46311645545510.027100
13.64-45.7115.7410.02643.7215272902660.9990.02991.7

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3546: ???)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TSZ

4tsz


Resolution: 3.05→45.711 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.87
RfactorNum. reflection% reflection
Rfree0.2236 2003 10.21 %
Rwork0.1898 --
obs0.1934 19613 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.65 Å2 / Biso mean: 86.6256 Å2 / Biso min: 40.77 Å2
Refinement stepCycle: final / Resolution: 3.05→45.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 5 9 2853
Biso mean--150.18 74.68 -
Num. residues----380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.05-3.12620.45231250.3641224100
3.1262-3.21070.42281390.31351234100
3.2107-3.30520.31971510.27081225100
3.3052-3.41180.27811270.24061238100
3.4118-3.53370.28981280.22821249100
3.5337-3.67510.28381410.21941248100
3.6751-3.84230.24751520.19981219100
3.8423-4.04480.22571570.18261227100
4.0448-4.2980.21341320.16521261100
4.298-4.62960.18551430.14571266100
4.6296-5.09490.17551540.14211247100
5.0949-5.83090.19981480.17971287100
5.8309-7.34140.22451530.19521293100
7.3414-45.7110.18761530.1805139299
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)
12.54370.85860.15924.6566-0.47094.1232-0.049-0.4163-0.02270.08120.14910.4256-0.1107-0.6327-0.11350.42990.19680.02830.86030.02620.606910.071154.611849.8809
20.70690.2565-0.46211.2674-0.36035.2845-0.0836-0.09840.23040.0613-0.01070.3454-0.1829-0.67770.02360.47390.1981-0.13571.04890.01490.8212.278860.24921.8959
34.4685-1.487-1.45264.828-0.71395.07350.10620.2213-0.0808-0.4007-0.1090.07670.2891-0.0173-0.06180.51360.139-0.14620.7766-0.07230.531516.63249.53321.5906
44.81042.45743.47095.5817-1.17164.50990.3504-0.5031.2676-0.54610.08490.8598-0.1661-0.5476-0.48220.56020.2709-0.01270.97460.0811.059810.922471.02587.7611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 125 )A-1 - 125
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 254 )A126 - 254
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 367 )A255 - 367
4X-RAY DIFFRACTION4chain 'G' and (resid 5 through 11 )G5 - 11

+
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