[English] 日本語
Yorodumi
- PDB-7k5s: Bst DNA polymerase I time-resolved structure, 4 hr post dATP and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k5s
TitleBst DNA polymerase I time-resolved structure, 4 hr post dATP and dCTP addition
Components
  • DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
  • DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / double-strand break repair / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain ...DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsChim, N. / Meza, R.A. / Trinh, A.M. / Chaput, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 2001434 United States
CitationJournal: Nat Commun / Year: 2021
Title: Following replicative DNA synthesis by time-resolved X-ray crystallography.
Authors: Chim, N. / Meza, R.A. / Trinh, A.M. / Yang, K. / Chaput, J.C.
History
DepositionSep 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')
T: DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3')
A: DNA polymerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8046
Polymers74,5153
Non-polymers2883
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-53 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.622, 93.416, 105.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: DNA chain DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3')


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3')


Mass: 4923.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein DNA polymerase I / Bst DNA polymerase I


Mass: 66233.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: polA / Production host: Escherichia coli (E. coli) / References: UniProt: E1C9K5, DNA-directed DNA polymerase
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50% ammonium sulfate, 0.1M MES, 2% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→46.05 Å / Num. obs: 99196 / % possible obs: 98.09 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0549 / Rpim(I) all: 0.0235 / Rrim(I) all: 0.05983 / Net I/σ(I): 18.14
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 0.8071 / Num. unique obs: 9747 / CC1/2: 0.849 / Rpim(I) all: 0.3296 / Rrim(I) all: 0.8728

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DSY

6dsy


Resolution: 1.67→46.05 Å / SU ML: 0.1712 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5838 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2096 1978 2.01 %
Rwork0.1868 96202 -
obs0.1872 98180 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.15 Å2
Refinement stepCycle: LAST / Resolution: 1.67→46.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 488 10 583 5722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615277
X-RAY DIFFRACTIONf_angle_d0.81537236
X-RAY DIFFRACTIONf_chiral_restr0.0504813
X-RAY DIFFRACTIONf_plane_restr0.005855
X-RAY DIFFRACTIONf_dihedral_angle_d9.95763145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.30531460.25686801X-RAY DIFFRACTION98.61
1.71-1.760.23371370.22066832X-RAY DIFFRACTION98.42
1.76-1.810.22371510.21416838X-RAY DIFFRACTION98.95
1.81-1.870.26261300.21886852X-RAY DIFFRACTION98.6
1.87-1.940.45681330.3566281X-RAY DIFFRACTION90.52
1.94-2.010.21851340.19866914X-RAY DIFFRACTION99.06
2.01-2.10.20391360.18016889X-RAY DIFFRACTION99.15
2.1-2.210.20811430.18116897X-RAY DIFFRACTION99.09
2.21-2.350.27181420.2336545X-RAY DIFFRACTION93.59
2.35-2.540.23031420.18796947X-RAY DIFFRACTION99.38
2.54-2.790.20371370.19367004X-RAY DIFFRACTION99.54
2.79-3.190.21081460.18897009X-RAY DIFFRACTION99.55
3.19-4.020.18891470.16027068X-RAY DIFFRACTION99.3
4.02-46.050.161540.15887325X-RAY DIFFRACTION99.47
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)
12.97335393359-0.637184592025-0.1333725580133.28235906176-0.04049787532151.952077412510.09270510435610.867394672225-0.7087925808790.231217141261-0.336653727721-0.1650436911440.7664379972320.3890951835350.1601354166550.5423505521060.159506646094-0.02988619634420.513374888771-0.1397882746410.51822674490426.354065008830.998184041534.4824348363
24.62906658662-0.376933728826-0.1813350571770.3913598816480.7020377889431.29268014133-0.347622361738-0.485925492368-0.422365724990.5059267604510.339493251549-0.329046473271.379582935820.6009057912980.1791725096870.6266018922080.257152207165-0.01940219979650.428097444875-0.03111449620130.4817297475425.064797752328.735828727936.0372445146
31.44691482670.677154011334-0.3205096096691.83075121572-0.1591180502181.01391755417-0.05811245607760.149793065249-0.109279246029-0.2550146732920.043454822531-0.09775430479680.08179267611410.008483734033110.00904829762340.218353971888-0.0139501851270.01460418165950.202403988791-0.01107391741940.185064327699.6873560470526.11202382945.76207058846
40.2848307095540.0358137759665-0.1590324512221.38723856347-0.6267353672741.40955335234-0.09862505550830.05158583479270.2540359322650.0968119556277-0.0538238126011-0.172177728652-0.1033462398820.3995734930450.176340983250.2120818870580.01580246482010.02075357178130.241965155641-0.0355096197880.18261706818724.340016426543.554424742325.4713257744
50.835437506717-0.6686018763892.214319994871.38415422417-0.7224799599934.21933982165-0.0168600156352-0.0882094285048-0.01213070065240.5480114605430.116290184966-0.172124717280.3399596007820.185344540369-0.07389514116840.4985703459560.0930750332993-0.04155514759130.3972270788630.02418822852140.3041244778435.388442248636.882409767340.2348760863
60.885107766283-0.0916675258788-0.7156661754240.829649707455-0.08427524008191.071118057550.0145621260452-0.04321121863440.0955153539070.041077918403-0.0145438765386-0.0868922495024-0.06880459360650.07508003288660.003242878397510.174994156263-0.00969167970596-0.01498660015630.1758091190610.006754756239460.18482143059612.680181805346.942784774130.7345561918
72.686378461610.380308076931.075304287432.635513769549.4797628198E-52.011925437240.00348967088784-0.139144259709-0.1442082212360.3533581576070.00675800344089-0.1974436765450.0961609351180.0321628465638-0.018951866490.2506767214320.0154224190287-0.0273247840570.223376236614-0.003803545508510.1996811562418.2814959552144.200753630853.5796968442
80.7821743542580.429574331153-0.3462502299191.24847419829-0.3012691236770.8643175926210.0662307262692-0.01649444681050.01650498674370.0753363683374-0.04228532248050.02439530785670.0123688148528-0.0276579843897-0.03774106072640.162720845001-0.00574504025728-0.001226736958790.174574140869-0.007792049930160.1745057650864.717025604643.283985176330.3611009967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'P' and (resid 2 through 11 )
2X-RAY DIFFRACTION2chain 'T' and (resid 2 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 300 through 467 )
4X-RAY DIFFRACTION4chain 'A' and (resid 468 through 522 )
5X-RAY DIFFRACTION5chain 'A' and (resid 523 through 604 )
6X-RAY DIFFRACTION6chain 'A' and (resid 605 through 676 )
7X-RAY DIFFRACTION7chain 'A' and (resid 677 through 743 )
8X-RAY DIFFRACTION8chain 'A' and (resid 744 through 876 )

+
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