[English] 日本語
Yorodumi
- PDB-9yd1: Crystal structure of BF DNA polymerase F710Y mutant bound to tetr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yd1
TitleCrystal structure of BF DNA polymerase F710Y mutant bound to tetrahydrofuran and dATP
Components
  • DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
  • DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
  • DNA polymerase I
KeywordsREPLICATION
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 / DNA polymerase A / DNA polymerase family A / 3'-5' exonuclease / 3'-5' exonuclease domain / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain ...: / DNA polymerase I, ribonuclease H-like domain / DNA polymerase 1 / DNA polymerase A / DNA polymerase family A / 3'-5' exonuclease / 3'-5' exonuclease domain / 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
sucrose / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase I
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsWu, E.Y. / Beese, L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM091487 United States
CitationJournal: Biochemistry / Year: 2026
Title: Structural basis for blockage of DNA synthesis by a thymine dimer lesion in a high-fidelity DNA polymerase
Authors: Walsh, A.R. / Beese, L.S. / Wu, E.Y.
History
DepositionSep 20, 2025Deposition site: RCSB / Processing site: RCSB
SupersessionJun 24, 2026ID: 6UEU
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase I
D: DNA polymerase I
B: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
C: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
E: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
F: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,67912
Polymers144,7986
Non-polymers1,8816
Water15,583865
1
A: DNA polymerase I
B: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
C: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2325
Polymers72,3993
Non-polymers8332
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-12 kcal/mol
Surface area27590 Å2
MethodPISA
2
D: DNA polymerase I
E: DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')
F: DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4477
Polymers72,3993
Non-polymers1,0484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-13 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.875, 109.068, 150.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(2DT))-3')


Mass: 2699.800 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*(3DR)P*AP*CP*GP*TP*GP*AP*TP*CP*G)-3')


Mass: 3554.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein / Sugars , 2 types, 4 molecules AD

#1: Protein DNA polymerase I


Mass: 66144.836 Da / Num. of mol.: 2 / Mutation: F710Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: DPO1, polA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D9N168, DNA-directed DNA polymerase
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 869 molecules

#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50% (v/v) saturated ammonium sulfate, 20 mM MgSO4, 100 mM MES, 1% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.987 Å / Num. obs: 138448 / % possible obs: 96.9 % / Redundancy: 4.572 % / Biso Wilson estimate: 21.36 Å2 / Rmerge F obs: 0.132 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.089 / Net I/σ(I): 12.27 / Num. measured all: 632948
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.94.4680.6140.5952.799419121153210820.67899.7
1.9-2.194.5050.3120.2945.4118757041816416320.33599.6
2.19-2.44.5540.1560.1599.448502818955186700.1898.5
2.4-2.684.5950.1040.10713.047578916960164950.12197.3
2.68-3.14.6520.0650.07417.556764615331145400.08494.8
3.1-3.794.6760.0360.0524.845527912797118220.05792.4
3.79-5.344.7250.0260.04132.04430751002391160.04591
5.34-44.9874.7870.0220.03735.8824370583150910.04187.3

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementResolution: 1.8→44.987 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 6922 5 %
Rwork0.2003 --
obs0.2024 138444 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: final / Resolution: 1.8→44.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 828 119 865 11116
Biso mean--36.23 34.32 -
Num. residues----1202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01810521
X-RAY DIFFRACTIONf_angle_d1.34714404
X-RAY DIFFRACTIONf_dihedral_angle_d18.3666252
X-RAY DIFFRACTIONf_chiral_restr0.0821619
X-RAY DIFFRACTIONf_plane_restr0.011706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.32522340.28984452X-RAY DIFFRACTION99
1.8205-1.84190.3242350.28274463X-RAY DIFFRACTION100
1.8419-1.86430.29112340.27034435X-RAY DIFFRACTION100
1.8643-1.88790.3072360.26884495X-RAY DIFFRACTION100
1.8879-1.91280.30372370.26414490X-RAY DIFFRACTION100
1.9128-1.9390.31422340.25134446X-RAY DIFFRACTION100
1.939-1.96670.28412350.24024474X-RAY DIFFRACTION100
1.9667-1.9960.26682360.23324477X-RAY DIFFRACTION100
1.996-2.02720.26692350.22434464X-RAY DIFFRACTION100
2.0272-2.06050.26452350.21564474X-RAY DIFFRACTION99
2.0605-2.0960.26762350.21644459X-RAY DIFFRACTION99
2.096-2.13410.25262350.20834475X-RAY DIFFRACTION100
2.1341-2.17520.25972350.20564450X-RAY DIFFRACTION99
2.1752-2.21960.24442330.2034439X-RAY DIFFRACTION99
2.2196-2.26780.25972330.20134430X-RAY DIFFRACTION99
2.2678-2.32060.23242340.19024438X-RAY DIFFRACTION99
2.3206-2.37860.23332330.19164432X-RAY DIFFRACTION98
2.3786-2.44290.24562320.19394401X-RAY DIFFRACTION98
2.4429-2.51480.24052310.19094389X-RAY DIFFRACTION97
2.5148-2.59590.23842320.18874413X-RAY DIFFRACTION97
2.5959-2.68870.25092290.1914354X-RAY DIFFRACTION97
2.6887-2.79640.24822290.1954348X-RAY DIFFRACTION96
2.7964-2.92360.24232270.19144303X-RAY DIFFRACTION95
2.9236-3.07770.23072230.19734235X-RAY DIFFRACTION94
3.0777-3.27050.24982240.18884253X-RAY DIFFRACTION93
3.2705-3.52290.20932210.17864209X-RAY DIFFRACTION92
3.5229-3.87720.20952220.1734210X-RAY DIFFRACTION92
3.8772-4.43790.22352210.17664201X-RAY DIFFRACTION91
4.4379-5.58960.20652210.18244195X-RAY DIFFRACTION90
5.5896-45.00090.24232210.21624218X-RAY DIFFRACTION87

+
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