[English] 日本語
Yorodumi
- PDB-6fx7: Crystal structure of in vitro evolved Af1521 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fx7
TitleCrystal structure of in vitro evolved Af1521
Components[Protein ADP-ribosylglutamate] hydrolase AF_1521
KeywordsSIGNALING PROTEIN / Macro domain / ADP-ribose binding
Function / homology
Function and homology information


ADP-ribosylglutamate hydrolase activity / peptidyl-glutamate ADP-deribosylation / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
Similarity search - Function
Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / ADP-ribose glycohydrolase AF_1521
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsKarlberg, T. / Thorsell, A.G. / Nowak, K. / Hottiger, M.O. / Schuler, H.
CitationJournal: Nat Commun / Year: 2020
Title: Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins.
Authors: Nowak, K. / Rosenthal, F. / Karlberg, T. / Butepage, M. / Thorsell, A.G. / Dreier, B. / Grossmann, J. / Sobek, J. / Imhof, R. / Luscher, B. / Schuler, H. / Pluckthun, A. / Leslie Pedrioli, D.M. / Hottiger, M.O.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: [Protein ADP-ribosylglutamate] hydrolase AF_1521
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1352
Polymers23,5761
Non-polymers5591
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.312, 39.535, 35.964
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein [Protein ADP-ribosylglutamate] hydrolase AF_1521


Mass: 23575.941 Da / Num. of mol.: 1
Mutation: K15R, K35E, Y74C, F97L, I103V, S105G, E110G, Y145R, N162D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: AF_1521 / Plasmid: pET19b / Production host: Escherichia coli (E. coli)
References: UniProt: O28751, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 %w/v PEG3350, 0,2M sodium chloride, 0.1 M bis-tris, 2mM ADP-ribose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.82→70.02 Å / Num. obs: 17843 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.119 / Rrim(I) all: 0.221 / Net I/σ(I): 8.6
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.528 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 841 / CC1/2: 0.53 / Rpim(I) all: 1.796 / Rrim(I) all: 3.116 / % possible all: 96

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROC1.0.5data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BFQ

2bfq


Resolution: 1.82→70.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.212 849 4.78 %RANDOM
Rwork0.187 ---
obs0.188 17778 99.2 %-
Displacement parametersBiso mean: 30.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.6496 Å20 Å25.2261 Å2
2---4.2852 Å20 Å2
3---6.9347 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.82→70.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 36 100 1612
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011573HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.022128HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d760SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1573HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion203SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1870SEMIHARMONIC4
LS refinement shellResolution: 1.82→1.93 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2258 137 4.96 %
Rwork0.2134 2627 -
all0.214 2764 -
obs--96.11 %
Refinement TLS params.Method: refined / Origin x: -20.5563 Å / Origin y: -16.8081 Å / Origin z: 6.8698 Å
111213212223313233
T-0.0542 Å20.0214 Å2-0.0083 Å2--0.062 Å2-0.0447 Å2---0.066 Å2
L2.5334 °2-0.8507 °20.2295 °2-1.247 °2-0.0702 °2--1.6886 °2
S-0.1233 Å °-0.2603 Å °0.1402 Å °0.0952 Å °0.1157 Å °-0.1025 Å °-0.0412 Å °0.0405 Å °0.0076 Å °
Refinement TLS groupSelection details: { A|* }

+
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