[English] 日本語
Yorodumi
- PDB-8ild: The crystal structure of native dGTP:DNApre-I:Pol X substrate ter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ild
TitleThe crystal structure of native dGTP:DNApre-I:Pol X substrate ternary complex
Components
  • DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T)-3')
  • Repair DNA polymerase X
KeywordsREPLICATION/DNA / DNA polymerase / substrate complex / REPLICATION-DNA complex
Function / homology
Function and homology information


virion component / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding
Similarity search - Function
Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / DNA / Repair DNA polymerase X
Similarity search - Component
Biological speciesAfrican swine fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsQin, T. / Chen, Y.Q. / Gan, J.H. / Huang, Z.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)22077089 China
National Natural Science Foundation of China (NSFC)22107079 China
Ministry of Education (MoE, China)2020M673205 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Authors: Qin, T. / Hu, B. / Zhao, Q. / Wang, Y. / Wang, S. / Luo, D. / Lyu, J. / Chen, Y. / Gan, J. / Huang, Z.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,99910
Polymers46,6514
Non-polymers1,3486
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-45 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.706, 75.441, 108.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein Repair DNA polymerase X / Pol X / AsfvPolX


Mass: 20609.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (strain Badajoz 1971 Vero-adapted)
Gene: Ba71V-97, O174L / Production host: Escherichia coli (E. coli) / References: UniProt: P42494, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T)-3')


Mass: 2715.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 81 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: Ammonium acetate (0.2 M), BIS-Tris pH=5.5 (0.1 M), 20% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 21028 / % possible obs: 93.5 % / Redundancy: 5.1 % / CC1/2: 0.814 / Net I/σ(I): 26.6
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 1477 / CC1/2: 0.256

-
Processing

Software
NameVersionClassification
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→28.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 18.726 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26325 1128 5.1 %RANDOM
Rwork0.21216 ---
obs0.21494 21028 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.861 Å2
Baniso -1Baniso -2Baniso -3
1-6.97 Å20 Å2-0 Å2
2---5.53 Å20 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 2.25→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 358 74 75 3270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0183298
X-RAY DIFFRACTIONr_bond_other_d0.0020.023079
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9064529
X-RAY DIFFRACTIONr_angle_other_deg1.06437043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1755349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79722.885104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0051518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02725
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.70936377
X-RAY DIFFRACTIONr_sphericity_free74.507525
X-RAY DIFFRACTIONr_sphericity_bonded10.19156328
Refine LS restraints NCS

Ens-ID: 1 / Number: 10533 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 97 -
Rwork0.3 1477 -
obs--93.03 %
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)
11.09730.0514-0.39631.7982-0.23431.3441-0.06170.0169-0.1133-0.01010.03170.0877-0.0215-0.020.030.0065-0.00560.02130.27970.01290.21318.634412.64342.5943
21.4274-0.543-0.26921.32170.32082.99950.1045-0.08870.1913-0.1993-0.01970.0092-0.18630.0621-0.08480.0433-0.0399-0.00510.2542-0.01280.217117.825734.66186.6896
32.3061-0.50110.11952.17310.80981.879-0.04210.22010.02770.0013-0.0644-0.3576-0.24820.47160.10660.0407-0.074-0.05110.31750.04190.211552.262921.352230.4832
41.1019-0.32930.58832.50110.8433.6612-0.2403-0.35720.09260.0109-0.0630.1564-0.1052-0.2290.30330.05660.067-0.01460.2651-0.0130.203833.888826.485941.4251
50.7118-0.31390.92840.2171-0.56341.5204-0.0663-0.04590.01770.07480.0539-0.0146-0.1668-0.08210.01240.06140.025-0.05070.3396-0.0560.243731.309820.307917.6176
61.29170.31790.89980.4593-0.67392.7619-0.11040.0978-0.09450.0012-0.0051-0.0644-0.14770.15210.11550.07410.0246-0.00370.2552-0.0010.232433.961121.093719.9149
715.226-9.60037.382914.6696-0.32186.1492-0.2843-0.53960.14720.28260.2884-0.178-0.1073-0.4182-0.00410.13020.01970.02390.1804-0.00250.134938.947115.818133.9969
83.2075-1.0737-2.60289.54727.45846.84110.0907-0.0534-0.09020.0402-0.36430.2542-0.0369-0.24610.27360.0919-0.0137-0.04540.2926-0.0490.24827.039824.94293.0111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 105
2X-RAY DIFFRACTION2A106 - 174
3X-RAY DIFFRACTION3B0 - 105
4X-RAY DIFFRACTION4B106 - 174
5X-RAY DIFFRACTION5C1 - 9
6X-RAY DIFFRACTION6D1 - 9
7X-RAY DIFFRACTION7B201
8X-RAY DIFFRACTION8A201

+
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