[English] 日本語
Yorodumi
- PDB-7r2g: USP15 D1D2 in catalytically-competent state bound to mitoxantrone... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7r2g
TitleUSP15 D1D2 in catalytically-competent state bound to mitoxantrone stack (isoform 2)
ComponentsUbiquitin carboxyl-terminal hydrolase 15
KeywordsHYDROLASE / Cysteine protease
Function / homologyChem-MIX
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPriyanka, A. / Sixma, T.K.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)NWO-LIFT 731.017.415 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Mitoxantrone stacking does not define the active or inactive state of USP15 catalytic domain.
Authors: Priyanka, A. / Tisi, D. / Sixma, T.K.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 15
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,62517
Polymers83,0682
Non-polymers5,55715
Water2,378132
1
A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5992
Polymers41,5341
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,02515
Polymers41,5341
Non-polymers5,49114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.882, 97.399, 62.995
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 15


Mass: 41534.000 Da / Num. of mol.: 2 / Mutation: No
Source method: isolated from a genetically manipulated source
Details: aa 255 to 919 Internal deletion of residues 440 to 756 Construct has C terminal 6X his tag
Source: (gene. exp.) Homo sapiens (human) / Gene: USP15 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1 resistant / References: ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MIX / 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)-9,10-ANTHRACENEDIONE / MITOXANTRONE / 1,4-DIHYDROXY-5,8-BIS({2-[(2-HYDROXYETHYL)AMINO]ETHYL}AMINO)ANTHRA-9,10-QUINONE


Mass: 444.481 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C22H28N4O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antineoplastic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium Hepes 0.1M, pH 7.0, PEG8000 5%. / PH range: 6.8-7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019 / Details: X-ray
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→97.4 Å / Num. obs: 51964 / % possible obs: 97 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.023 / Rrim(I) all: 0.045 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.98-2.0340.2351352934090.9630.1340.2725.190.7
9.07-44.863.80.0321955760.9970.0170.03440.898.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSVERSION Mar 15, 2019 BUILT=20190606data reduction
XDSVERSION Mar 15, 2019 BUILT=20190606data scaling
PHASER2.8.3phasing
Coot0.9.6 ELmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gha

6gha


Resolution: 1.98→44.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.238 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 2444 4.7 %RANDOM
Rwork0.2041 ---
obs0.2057 49498 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.49 Å2 / Biso mean: 51.027 Å2 / Biso min: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å20.51 Å2
2--9.84 Å2-0 Å2
3----4.93 Å2
Refinement stepCycle: final / Resolution: 1.98→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 392 132 6128
Biso mean--112.56 40.59 -
Num. residues----697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136169
X-RAY DIFFRACTIONr_bond_other_d0.0040.0155598
X-RAY DIFFRACTIONr_angle_refined_deg1.511.6448345
X-RAY DIFFRACTIONr_angle_other_deg1.341.5912959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21723.627306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99415975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5671523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026925
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021405
LS refinement shellResolution: 1.98→2.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 150 -
Rwork0.278 3448 -
all-3598 -
obs--90.52 %
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)
11.4877-0.3608-0.05570.51430.20091.60080.03130.1890.0143-0.0294-0.1057-0.0104-0.0941-0.02750.07450.42440.0085-0.02010.03250.00830.461131.179-17.0847.687
21.63710.185-0.07750.39870.03971.5984-0.0362-0.2184-0.0436-0.0089-0.0927-0.01280.10410.08770.12890.43370.0027-0.02360.04620.01710.4747-0.509-30.72-20.639
30.60190.22780.8270.1430.30821.327-0.0381-0.01780.085-0.0257-0.02230.0152-0.0417-0.05410.06050.46580.0185-0.00240.0107-0.00220.519.039-23.61-14.179
41.18880.19130.81480.5298-0.080.7204-0.23190.42180.21450.0064-0.00770.15350.02790.27180.23971.0252-0.02010.22560.5173-0.28430.529812.297-56.089-53.423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A255 - 1001
2X-RAY DIFFRACTION2B255 - 1001
3X-RAY DIFFRACTION3A1101 - 1152
4X-RAY DIFFRACTION4B1003 - 1014
5X-RAY DIFFRACTION3B1101 - 1180

+
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