[English] 日本語
Yorodumi
- PDB-9r40: HaloTag bound to compound MRC71 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r40
TitleHaloTag bound to compound MRC71
ComponentsHaloalkane dehalogenase
KeywordsLIGASE / TRIM21 / E3 ligase / PROTAC / PRYSPRY / Halotag
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.043 Å
AuthorsLuptak, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: Development of TRIM21 PROTAC molecules
Authors: Luptak, J. / James, L.C.
History
DepositionMay 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6593
Polymers34,8071
Non-polymers8522
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.797, 62.797, 163.274
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Haloalkane dehalogenase


Mass: 34806.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N terminally his-tagged HaloTag7
Source: (gene. exp.) Rhodococcus sp. (in: high G+C Gram-positive bacteria) (bacteria)
Gene: dhaA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P0A3G3, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-A1JC1 / (2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(2-methoxyphenyl)propanoyl]-~{N}-[(2~{R})-1-[2-[2-[2-[2-(6-chloranylhexoxy)ethoxy]ethoxy]ethoxy]ethylamino]-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]-4-cyclohexyl-pyrrolidine-2-carboxamide


Mass: 816.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H66ClN5O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 4000, 0.1 M Na MES pH 6.5, 0.2 M Mg Chloride.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.04→58.68 Å / Num. obs: 21548 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 1 / Net I/σ(I): 4.8
Reflection shellResolution: 2.04→2.08 Å / Num. unique obs: 990 / CC1/2: 0.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.043→58.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.338 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / ESU R: 0.234 / ESU R Free: 0.205
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2861 1048 4.879 %
Rwork0.2373 20431 -
all0.24 --
obs-21479 99.634 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.043 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å2-0 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.043→58.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 57 43 2451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122457
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162296
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.8133357
X-RAY DIFFRACTIONr_angle_other_deg0.5471.745305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2455296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.83517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72410375
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.60110116
X-RAY DIFFRACTIONr_chiral_restr0.0730.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02561
X-RAY DIFFRACTIONr_nbd_refined0.2160.2616
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22421
X-RAY DIFFRACTIONr_nbtor_refined0.190.21195
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21284
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.290.28
X-RAY DIFFRACTIONr_nbd_other0.2110.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.27
X-RAY DIFFRACTIONr_mcbond_it2.9563.8711175
X-RAY DIFFRACTIONr_mcbond_other2.9573.8711175
X-RAY DIFFRACTIONr_mcangle_it4.3636.9511468
X-RAY DIFFRACTIONr_mcangle_other4.3666.9521469
X-RAY DIFFRACTIONr_scbond_it2.9913.9231282
X-RAY DIFFRACTIONr_scbond_other2.993.9231283
X-RAY DIFFRACTIONr_scangle_it4.6737.1711887
X-RAY DIFFRACTIONr_scangle_other4.6717.171888
X-RAY DIFFRACTIONr_lrange_it6.99937.3322817
X-RAY DIFFRACTIONr_lrange_other7.00337.3482815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.043-2.0960.438900.45114040.4515660.8430.86295.40230.467
2.096-2.1540.467660.41114220.41314950.8260.84299.53180.428
2.154-2.2160.41740.3814040.38214780.8120.8471000.387
2.216-2.2840.414690.3613620.36214310.8390.8641000.364
2.284-2.3590.358750.34813320.34814070.8770.8731000.345
2.359-2.4410.387560.3312820.33213380.8760.891000.324
2.441-2.5330.303580.30212480.30213060.9240.9141000.287
2.533-2.6370.338770.2911860.29312630.9040.9261000.265
2.637-2.7540.32550.26611660.26812210.9350.9461000.236
2.754-2.8880.365600.26810970.27211570.9120.951000.231
2.888-3.0440.338510.23610530.24111040.9330.9591000.2
3.044-3.2280.289540.2219970.22510510.9460.9641000.183
3.228-3.450.342560.2099550.21610110.9320.9691000.181
3.45-3.7250.27420.1949020.1979440.9490.9761000.176
3.725-4.0790.209380.1798170.1818550.9780.9811000.161
4.079-4.5580.183380.1427620.1448000.9850.9891000.126
4.558-5.2580.193400.1326730.1357130.9750.9891000.115
5.258-6.4260.238140.1645960.1656100.9790.9831000.14
6.426-9.0340.178200.1734770.1734970.9820.9821000.157
9.034-58.680.164150.2062960.2043110.9850.971000.214

+
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