[English] 日本語
Yorodumi
- PDB-8c8b: Crystal structure of human DNA cross-link repair 1A in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c8b
TitleCrystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 48).
ComponentsDNA cross-link repair 1A protein
KeywordsHYDROLASE / exonuclease / SNM1A / nuclease inhibition
Function / homology
Function and homology information


5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / damaged DNA binding / cell division / nucleoplasm / metal ion binding
Similarity search - Function
DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-U1L / DNA cross-link repair 1A protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsYosaatmadja, Y. / Newman, J.A. / Baddock, H.T. / Bielinski, M. / von Delft, F. / Bountra, C. / McHugh, P.J. / Schofield, C.J. / Gileadi, O.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 21).
Authors: Yosaatmadja, Y. / Newman, J.A. / Baddock, H.T. / Bielinski, M. / von Delft, F. / Bountra, C. / McHugh, P.J. / Schofield, C.J. / Gileadi, O.
History
DepositionJan 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA cross-link repair 1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3684
Polymers38,9221
Non-polymers4463
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-46 kcal/mol
Surface area15630 Å2
Unit cell
Length a, b, c (Å)51.690, 57.250, 113.520
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: Protein DNA cross-link repair 1A protein / Beta-lactamase DCLRE1A / SNM1 homolog A / hSNM1 / hSNM1A


Mass: 38922.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1A, KIAA0086, SNM1, SNM1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PJP8, beta-lactamase
#2: Chemical ChemComp-U1L / 4-[[(2~{S})-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-~{N}-prop-2-enyl-quinazoline-2-carboxamide


Mass: 315.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% PEG 1000, 0.1M MIB buffer

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.46→51.12 Å / Num. obs: 57993 / % possible obs: 98 % / Redundancy: 13.6 % / Biso Wilson estimate: 23.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Net I/σ(I): 19.4
Reflection shellResolution: 1.46→1.5 Å / Rmerge(I) obs: 3.108 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4073 / CC1/2: 0.356 / Rpim(I) all: 0.915 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→36.35 Å / SU ML: 0.1909 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 2858 4.93 %
Rwork0.1946 55071 -
obs0.1958 57929 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.27 Å2
Refinement stepCycle: LAST / Resolution: 1.46→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 25 251 2970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432834
X-RAY DIFFRACTIONf_angle_d0.72623860
X-RAY DIFFRACTIONf_chiral_restr0.0741428
X-RAY DIFFRACTIONf_plane_restr0.0046488
X-RAY DIFFRACTIONf_dihedral_angle_d17.73521029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.32211240.35222615X-RAY DIFFRACTION94.03
1.49-1.510.31341440.31482654X-RAY DIFFRACTION95.66
1.51-1.540.34121280.30112694X-RAY DIFFRACTION96.78
1.54-1.570.31391400.28672699X-RAY DIFFRACTION96.76
1.57-1.610.30811380.27942681X-RAY DIFFRACTION96.67
1.61-1.640.25381430.26162709X-RAY DIFFRACTION97.07
1.64-1.690.29341260.24082716X-RAY DIFFRACTION96.86
1.69-1.730.24061430.23992707X-RAY DIFFRACTION97.34
1.73-1.780.26021420.23672732X-RAY DIFFRACTION97.59
1.78-1.840.26571440.22612736X-RAY DIFFRACTION97.66
1.84-1.910.22561170.21242754X-RAY DIFFRACTION97.82
1.91-1.980.23541560.20622733X-RAY DIFFRACTION98.03
1.98-2.070.23451550.19692755X-RAY DIFFRACTION98.54
2.07-2.180.24181440.19632765X-RAY DIFFRACTION98.54
2.18-2.320.20521570.19862769X-RAY DIFFRACTION98.39
2.32-2.50.2451420.19292809X-RAY DIFFRACTION98.73
2.5-2.750.21191430.19782827X-RAY DIFFRACTION99.17
2.75-3.140.22471570.20172816X-RAY DIFFRACTION99.43
3.15-3.960.19561310.17532905X-RAY DIFFRACTION99.44
3.96-36.350.18091840.16052995X-RAY DIFFRACTION99.5

+
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://pdbjlvh1.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