[English] 日本語
Yorodumi
- PDB-6y4z: The crystal structure of human MACROD2 in space group P43212 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y4z
TitleThe crystal structure of human MACROD2 in space group P43212
ComponentsThioredoxin 1,ADP-ribose glycohydrolase MACROD2
KeywordsHYDROLASE / ADP-ribosylhydrolase / macrodomain
Function / homology
Function and homology information


peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA polymerase processivity factor activity ...peptidyl-glutamate ADP-deribosylation / ADP-ribosylglutamate hydrolase activity / protein de-ADP-ribosylation / purine nucleoside metabolic process / O-acetyl-ADP-ribose deacetylase activity / deacetylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / response to bacterium / brain development / DNA damage response / nucleolus / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. ...Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like
Similarity search - Domain/homology
L(+)-TARTARIC ACID / ADP-ribose glycohydrolase MACROD2 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWazir, S. / Maksimainen, M.M. / Lehtio, L.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland287063 Finland
Academy of Finland294085 Finland
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Multiple crystal forms of human MacroD2.
Authors: Wazir, S. / Maksimainen, M.M. / Lehtio, L.
History
DepositionFeb 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
B: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
C: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
D: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7775
Polymers163,6274
Non-polymers1501
Water7,909439
1
A: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2


Theoretical massNumber of molelcules
Total (without water)40,9071
Polymers40,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2


Theoretical massNumber of molelcules
Total (without water)40,9071
Polymers40,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2


Theoretical massNumber of molelcules
Total (without water)40,9071
Polymers40,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0572
Polymers40,9071
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.360, 95.360, 261.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
Thioredoxin 1,ADP-ribose glycohydrolase MACROD2 / Trx-1 / MACRO domain-containing protein 2 / O-acetyl-ADP-ribose deacetylase MACROD2 / [Protein ADP- ...Trx-1 / MACRO domain-containing protein 2 / O-acetyl-ADP-ribose deacetylase MACROD2 / [Protein ADP-ribosylaspartate] hydrolase MACROD2 / [Protein ADP-ribosylglutamate] hydrolase MACROD2


Mass: 40906.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: trxA, fipA, tsnC, b3781, JW5856, MACROD2, C20orf133 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AA25, UniProt: A1Z1Q3, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→47.73 Å / Num. obs: 95967 / % possible obs: 100 % / Redundancy: 13.348 % / Biso Wilson estimate: 42.232 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Χ2: 1.046 / Net I/σ(I): 18.92 / Num. measured all: 1280920 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9511.3951.651.2579871701170090.7461.729100
1.95-212.9551.2571.987862678367820.8671.309100
2-2.0614.0740.9372.8193549664766470.9320.972100
2.06-2.1213.9620.7073.7290016644764470.9550.734100
2.12-2.1913.8790.5394.8586719625162480.9750.56100
2.19-2.2713.6360.416.2582868607760770.9860.426100
2.27-2.3613.0390.3257.575955582858250.9890.33899.9
2.36-2.4513.6780.289.1277690568156800.990.291100
2.45-2.5613.2310.21611.4671474540254020.9940.224100
2.56-2.6914.0190.18413.8772635518151810.9950.191100
2.69-2.8313.990.14117.9269391496049600.9970.146100
2.83-313.7610.10823.0164897471647160.9980.113100
3-3.2113.3480.07831.2959133443044300.9990.081100
3.21-3.4712.8580.05839.7853000412241220.9990.061100
3.47-3.812.9650.04848.3949798384138410.9990.05100
3.8-4.2513.8420.04156.57481153476347610.042100
4.25-4.9113.6780.03761.54424143101310110.038100
4.91-6.0112.880.03758.5134312266426640.9990.038100
6.01-8.512.3640.03260.63261492115211510.033100
8.5-47.7312.1160.02477.1415072125612440.9990.02599

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IQY

4iqy


Resolution: 1.9→47.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.095 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 4765 5 %RANDOM
Rwork0.2005 ---
obs0.2018 91202 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.45 Å2 / Biso mean: 42.981 Å2 / Biso min: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å2-0 Å2-0 Å2
2--1.68 Å2-0 Å2
3----3.37 Å2
Refinement stepCycle: final / Resolution: 1.9→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 10 440 7306
Biso mean--42.53 43.21 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137074
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176793
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6389541
X-RAY DIFFRACTIONr_angle_other_deg1.3671.58215766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44421.816358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.958151317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3531548
X-RAY DIFFRACTIONr_chiral_restr0.0780.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021481
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 339 -
Rwork0.353 6660 -
all-6999 -
obs--99.81 %

+
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