[English] 日本語
Yorodumi
- PDB-6dm6: Structure of DNA polymerase III subunit beta from Rickettsia cono... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dm6
TitleStructure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a natural product
Components
  • Beta sliding clamp
  • Natural product peptide
KeywordsTRANSFERASE / SSGCID / dnaN / DNA polymerase III subunit beta / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / 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 speciesRickettsia conorii (bacteria)
Streptomyces caelicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of DNA polymerase III subunit beta from Rickettsia conorii in complex with a natural product
Authors: Conrady, D.G. / Abendroth, J. / Higgins, T.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Structure summary
Category: pdbx_molecule_features / struct_site / struct_site_gen
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 / struct_ncs_dom_lim
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 / _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
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
B: Beta sliding clamp
C: Natural product peptide
D: Natural product peptide


Theoretical massNumber of molelcules
Total (without water)88,8604
Polymers88,8604
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-26 kcal/mol
Surface area33610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.860, 41.830, 127.400
Angle α, β, γ (deg.)90.000, 93.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 4 or (resid 5...
21(chain B and (resid -1 through 23 or resid 29...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISLEULEU(chain A and (resid -1 through 4 or (resid 5...AA-1 - 47 - 12
121ILEILEILEILE(chain A and (resid -1 through 4 or (resid 5...AA513
131HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
141HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
151HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
161HISHISVALVAL(chain A and (resid -1 through 4 or (resid 5...AA-1 - 3797 - 387
211HISHISGLUGLU(chain B and (resid -1 through 23 or resid 29...BB-1 - 237 - 31
221PROPROASPASP(chain B and (resid -1 through 23 or resid 29...BB29 - 5137 - 59
231TYRTYRVALVAL(chain B and (resid -1 through 23 or resid 29...BB53 - 7961 - 87
241HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
251HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
261HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
271HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
281HISHISVALVAL(chain B and (resid -1 through 23 or resid 29...BB-1 - 3797 - 387
112ACEACEGLYGLYchain CCC1 - 111 - 11
212ACEACEGLYGLYchain DDD1 - 111 - 11

NCS ensembles :
ID
1
2

-
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: 43314.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia conorii (strain ATCC VR-613 / Malish 7) (bacteria)
Strain: ATCC VR-613 / Malish 7 / Gene: dnaN, RC0583 / Plasmid: RicoA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92I37
#2: Protein/peptide Natural product peptide


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces caelicus (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Rigaku Wizard Cryo 1/2 A8: 0.1M Sodium cacodylate pH6.5, 35% 2-ethoxyethanol 0.4:0.4uL drops, direct cryo: tray 290984a8: puck mbp2-7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→49.017 Å / Num. obs: 42516 / % possible obs: 99.6 % / Redundancy: 3.725 % / Biso Wilson estimate: 36.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 1.022 / Net I/σ(I): 15.54 / Num. measured all: 158384 / Scaling rejects: 7
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
2.25-2.313.7750.5522.3911944317131640.8710.64599.8
2.31-2.373.7820.4562.8911315299529920.8880.53299.9
2.37-2.443.7840.4093.2911212296829630.9070.47899.8
2.44-2.523.7780.3443.8710908289028870.9220.40199.9
2.52-2.63.7860.2944.6410587279527960.9480.343100
2.6-2.693.780.2295.910160269826880.9630.26799.6
2.69-2.793.7790.197.139981264326410.9770.22299.9
2.79-2.93.7690.1518.789246246124530.9850.17699.7
2.9-3.033.7660.11811.319167244024340.9890.13899.8
3.03-3.183.7570.08514.728626230922960.9950.199.4
3.18-3.353.7280.06618.878167220321910.9960.07799.5
3.35-3.563.70.04823.967610206920570.9980.05699.4
3.56-3.83.6680.0427.97280199419850.9980.04699.5
3.8-4.113.6490.03232.46575181318020.9990.03899.4
4.11-4.53.6370.02638.176084168616730.9990.0399.2
4.5-5.033.650.02440.65599154315340.9990.02899.4
5.03-5.813.6150.02638.344945137613680.9990.03199.4
5.81-7.123.5510.02836.774137117211650.9990.03399.4
7.12-10.063.5010.01846.26318291690910.02199.2
10.06-49.0173.2030.01848.36165954251810.02195.6

-
Processing

Software
NameVersionClassification
PHENIXdev_3126refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DLK

6dlk


Resolution: 2.25→49.017 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.87
RfactorNum. reflection% reflection
Rfree0.2348 1978 4.66 %
Rwork0.1783 --
obs0.181 42486 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.45 Å2 / Biso mean: 47.8618 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 2.25→49.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5867 0 0 301 6168
Biso mean---47.02 -
Num. residues----777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2186X-RAY DIFFRACTION5.58TORSIONAL
12B2186X-RAY DIFFRACTION5.58TORSIONAL
21C26X-RAY DIFFRACTION5.58TORSIONAL
22D26X-RAY DIFFRACTION5.58TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2501-2.30640.26221220.217429193041100
2.3064-2.36870.25371460.227128522998100
2.3687-2.43840.31561320.224628532985100
2.4384-2.51710.28111380.216228833021100
2.5171-2.60710.30791400.215628973037100
2.6071-2.71150.27531260.208128682994100
2.7115-2.83490.31771320.209328983030100
2.8349-2.98430.27761690.199328643033100
2.9843-3.17120.24721520.2092831298399
3.1712-3.4160.25121370.19012885302299
3.416-3.75970.24451360.17432923305999
3.7597-4.30350.20331350.15542896303199
4.3035-5.42080.18181570.1352922307999
5.4208-49.0290.19111560.15573017317399
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)
17.5458-3.282-0.63126.0428-0.1844.93120.03310.17920.1658-0.1152-0.10920.0873-0.2268-0.12880.10990.2014-0.0426-0.00330.19290.00020.205-1.47993.9137-12.3151
24.8044-0.8587-1.06150.65590.30141.7030.0625-0.03420.2537-0.0137-0.06780.0385-0.0545-0.04010.01880.2609-0.018-0.03630.13930.01860.2453-13.19976.0105-9.2736
31.88210.04570.64910.81950.43241.7878-0.0248-0.0653-0.08070.0017-0.05770.15760.025-0.4670.0770.2411-0.0150.03360.3162-0.03260.3205-38.11913.8163-13.7765
47.18240.0029-3.28397.3773-2.60125.9775-0.01440.07710.1718-0.3286-0.0499-0.1366-0.2696-0.07810.08660.33220.0286-0.04250.3962-0.12820.2925-37.45511.5432-51.0718
54.0591-0.1616-0.7997-0.0023-0.02541.35040.07810.61340.1442-0.1623-0.15990.0762-0.0858-0.09860.05870.43910.0698-0.03040.33430.00420.295-22.27242.1063-55.8584
65.95980.6366-0.26450.37430.30391.6062-0.01510.40860.2043-0.0898-0.00530.12470.05240.05630.06190.41710.07070.01280.39730.06210.3419-15.16771.5418-59.3598
71.9407-0.0261.08631.89860.96494.22420.16070.3898-0.1145-0.1293-0.0215-0.15630.25430.4474-0.14390.34560.09570.02950.41140.02460.24398.3917-1.2056-41.8054
84.07881.7725-1.48666.06222.19273.8342-0.1856-0.62140.50631.26950.4643-1.0453-0.67520.2418-0.24790.68410.1528-0.26790.4838-0.12730.6927-42.747520.4582-11.0026
94.867-1.0176-0.63185.5643-1.07792.8347-0.27030.90570.6792-1.4877-0.01060.684-0.9821-0.55190.12470.62780.0444-0.13880.60610.18510.41345.239315.6628-55.101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 81 )A-1 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 172 )A82 - 172
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 379 )A173 - 379
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 81 )B-1 - 81
5X-RAY DIFFRACTION5chain 'B' and (resid 82 through 191 )B82 - 191
6X-RAY DIFFRACTION6chain 'B' and (resid 192 through 257 )B192 - 257
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 379 )B258 - 379
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )C1 - 11
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 11 )D1 - 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