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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6man
TitleCrystal structure of a DnaN sliding clamp DNA polymerase III subunit beta from Rickettsia bellii RML369-C
ComponentsBeta sliding clamp
KeywordsTRANSCRIPTION / National Institute of Allergy and Infectious Disease / NIAID / structural genomoics / DnaN / sliding clamp / polymerase / griselimycin / antibiotic / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
THIOCYANATE ION / Beta sliding clamp
Similarity search - Component
Biological speciesRickettsia bellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 Rickettsia bellii RML369-C
Authors: Edwards, T.E. / Conrady, D.G. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionAug 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9664
Polymers85,8462
Non-polymers1202
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-8 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.880, 81.740, 89.180
Angle α, β, γ (deg.)90.000, 92.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 3 or (resid 4...
21(chain B and (resid 0 through 12 or (resid 13...

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
11HISHISLYSLYS(chain A and (resid 0 through 3 or (resid 4...AA0 - 38 - 11
12VALVALILEILE(chain A and (resid 0 through 3 or (resid 4...AA4 - 512 - 13
13HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
14HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
15HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
16HISHISVALVAL(chain A and (resid 0 through 3 or (resid 4...AA0 - 3798 - 387
21HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB0 - 128 - 20
22GLNGLNALAALA(chain B and (resid 0 through 12 or (resid 13...BB13 - 1421 - 22
23HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387
24HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387
25HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387
26HISHISVALVAL(chain B and (resid 0 through 12 or (resid 13...BB-2 - 3796 - 387

-
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: 42923.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia bellii (strain RML369-C) (bacteria)
Strain: RML369-C / Gene: dnaN, RBE_0656 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RIS7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RibeA.17987.a.B1.PS38223 at 20 mg/mL against 26% PEG 3350, 0.25 M sodium thiocyanate, supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 301443e9, unique puck ID jka1-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→31.706 Å / Num. obs: 35239 / % possible obs: 99.8 % / Redundancy: 4.157 % / Biso Wilson estimate: 62.877 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Χ2: 1.01 / Net I/σ(I): 16.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.414.210.5962.7125800.8530.68199.9
2.41-2.484.2340.5033.1825400.8720.57599.9
2.48-2.554.2150.3824.1224780.9250.43799.9
2.55-2.634.240.2915.3623640.9570.33299.9
2.63-2.714.2140.2196.8823280.9770.251100
2.71-2.814.230.188.5422710.980.20599.9
2.81-2.914.2240.14310.3321370.9880.16399.9
2.91-3.034.1980.11112.9920800.9910.127100
3.03-3.174.2010.08316.1320010.9950.09599.8
3.17-3.324.1760.06419.6219060.9960.07399.8
3.32-3.54.1240.05323.5518380.9970.061100
3.5-3.724.0680.04726.4217210.9980.05499.8
3.72-3.974.0710.04129.416160.9970.047100
3.97-4.294.0670.03832.3315230.9970.04499.9
4.29-4.74.0370.03634.3513840.9980.04199.8
4.7-5.254.0750.03535.6312780.9980.0499.8
5.25-6.074.0540.03334.9711070.9970.03899.8
6.07-7.434.0640.03136.419670.9980.03599.9
7.43-10.513.9770.02737.537290.9980.03199.6
10.51-31.7063.550.02735.673910.9980.03191.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5w7z

5w7z


Resolution: 2.35→31.706 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.11
RfactorNum. reflection% reflection
Rfree0.2399 1760 5 %
Rwork0.1878 --
obs0.1904 35235 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.44 Å2 / Biso mean: 67.566 Å2 / Biso min: 28.6 Å2
Refinement stepCycle: final / Resolution: 2.35→31.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 11 124 5715
Biso mean--95.62 56.3 -
Num. residues----754
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2234X-RAY DIFFRACTION7.812TORSIONAL
12B2234X-RAY DIFFRACTION7.812TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.41350.33171470.262425332680100
2.4135-2.48450.30381380.262125662704100
2.4845-2.56470.31051410.239925532694100
2.5647-2.65630.29571300.237825802710100
2.6563-2.76260.34871240.236425492673100
2.7626-2.88820.27151340.237425852719100
2.8882-3.04040.31551420.252425432685100
3.0404-3.23070.3181500.245625682718100
3.2307-3.47990.29191130.230926142727100
3.4799-3.82950.26131510.190225442695100
3.8295-4.38240.23751210.156926082729100
4.3824-5.51670.1581300.136726082738100
5.5167-31.70870.17531390.15422624276399
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)
11.1525-0.48580.27123.9421-1.1091.61180.04490.14260.0672-0.1540.02510.22880.1126-0.013-0.05480.2899-0.0071-0.01340.3181-0.02030.4638-19.8276-2.8292-37.3175
24.31060.60431.59652.0476-0.39063.32340.1515-0.5908-0.33180.235-0.205-0.05940.42180.28550.02590.51650.03430.02990.43790.05680.4014-1.0288-23.4094-16.4936
33.08281.36791.01851.736-1.03062.64790.4515-0.8306-0.27740.3235-0.1658-0.29560.29960.0465-0.29460.7263-0.2129-0.11281.2786-0.04730.461722.78113.8358-4.4654
40.9311-0.36331.25042.5258-1.63973.18420.7447-0.9556-0.09580.7234-0.9635-0.40980.00420.886-0.17930.7721-0.3331-0.22941.55050.10010.46424.49451.1865-5.3156
52.1597-0.23321.0423.2243-1.71732.98650.1348-0.55050.47510.5504-0.1971-0.7746-0.36270.93470.21030.6338-0.25020.01671.2907-0.13460.55524.486619.203-13.7159
62.60770.14631.51633.2533-2.4794.20360.365-0.53790.33960.2395-0.1776-0.1151-0.29050.70320.01440.4611-0.16860.10680.6353-0.20950.568814.426328.1511-27.8564
72.1475-0.48961.02644.1262-1.29234.08560.17-1.14860.38820.3339-0.09940.2345-0.50160.65830.09940.4887-0.28110.04080.9272-0.15640.465818.144825.2568-18.1132
81.7319-0.75231.19213.4885-2.43493.62740.1525-0.90580.71090.6453-0.219-0.0878-0.75960.6030.14980.6473-0.25070.09221.0835-0.12810.541418.444227.0356-18.7807
93.39971.28930.83173.80830.79814.16920.19-0.15970.6194-0.2862-0.020.2157-0.3864-0.2082-0.15450.32130.01580.05980.26820.01310.6012-10.898522.2291-36.2598
104.46620.2059-0.10243.36050.75763.66530.1588-0.51150.86170.15540.01770.4137-0.5797-0.1087-0.09330.4581-0.03180.130.3273-0.09280.7413-5.042830.9856-30.5893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 140 )A0 - 140
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 379 )A141 - 379
3X-RAY DIFFRACTION3chain 'B' and (resid -2 through 22 )B-2 - 22
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 108 )B23 - 108
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 140 )B109 - 140
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 183 )B141 - 183
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 208 )B184 - 208
8X-RAY DIFFRACTION8chain 'B' and (resid 209 through 257 )B209 - 257
9X-RAY DIFFRACTION9chain 'B' and (resid 258 through 311 )B258 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 379 )B312 - 379

+
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://pdbjlc1.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