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- PDB-2rpz: Solution structure of the monomeric form of mouse APOBEC2 -

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Basic information

Entry
Database: PDB / ID: 2rpz
TitleSolution structure of the monomeric form of mouse APOBEC2
ComponentsProbable C->U-editing enzyme APOBEC-2
KeywordsHYDROLASE / cytidine deaminase / Metal-binding / mRNA processing / Zinc / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / mRNA(cytosine6666) deaminase / mRNA modification / cytidine to uridine editing / cytidine deaminase activity / DNA demethylation / mRNA processing / RNA binding / identical protein binding ...mRNA Editing: C to U Conversion / Formation of the Editosome / mRNA(cytosine6666) deaminase / mRNA modification / cytidine to uridine editing / cytidine deaminase activity / DNA demethylation / mRNA processing / RNA binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
C->U-editing enzyme APOBEC-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHayashi, F. / Nagata, T. / Nagashima, T. / Muto, Y. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the monomeric form of mouse APOBEC2
Authors: Hayashi, F. / Umehara, T. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 11, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable C->U-editing enzyme APOBEC-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9222
Polymers21,8571
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Probable C->U-editing enzyme APOBEC-2


Mass: 21856.650 Da / Num. of mol.: 1 / Fragment: UNP residues 46-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cell free Synthesis
References: UniProt: Q9WV35, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D HBHAHN
1913D (H)CCH-TOCSY
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 20 mM [U-2H] TRIS-1, 100 mM sodium chloride-2, 1 mM [U-2H] DTT-3, 0.02 % sodium azide-4, 0.1 mM ZINC ION-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRIS-1[U-2H]1
100 mMsodium chloride-21
1 mMDTT-3[U-2H]1
0.02 %sodium azide-41
100 uMZINC ION-51
Sample conditionsIonic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
KUJIRA0.9839Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, and Yokoyamadata analysis
KUJIRA0.9839Kobayashi, Iwahara, Koshiba, Tomizawa, Tochio, Guntert, Kigawa, and Yokoyamarefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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