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- PDB-2nyt: The APOBEC2 Crystal Structure and Functional Implications for AID -

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Basic information

Entry
Database: PDB / ID: 2nyt
TitleThe APOBEC2 Crystal Structure and Functional Implications for AID
ComponentsProbable C->U-editing enzyme APOBEC-2
KeywordsHYDROLASE / cytidine deaminase / zinc-ion binding / APOBEC
Function / homology
Function and homology information


mRNA(cytosine6666) deaminase / mRNA Editing: C to U Conversion / Formation of the Editosome / mRNA modification / cytidine to uridine editing / cytidine deaminase activity / : / mRNA processing / RNA binding / identical protein binding ...mRNA(cytosine6666) deaminase / mRNA Editing: C to U Conversion / Formation of the Editosome / mRNA modification / cytidine to uridine editing / cytidine deaminase activity / : / mRNA processing / RNA binding / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
APOBEC-like C-terminal domain / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsProchnow, C. / Bransteitter, R. / Klein, M. / Goodman, M. / Chen, X.
CitationJournal: Nature / Year: 2007
Title: The APOBEC-2 crystal structure and functional implications for the deaminase AID.
Authors: Prochnow, C. / Bransteitter, R. / Klein, M.G. / Goodman, M.F. / Chen, X.S.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,3778
Polymers87,1154
Non-polymers2624
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.841, 89.410, 245.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21778.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC2 / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90
References: UniProt: Q9Y235, 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 85mM NaCitrate, 160mM LiSO4, 24% (wt/vol) PEG, 15% glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9774, 0.9796, 0.9798
DetectorDetector: CCD / Date: Jan 15, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double CrystalSINGLE WAVELENGTHMx-ray1
2Double CrystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
20.97961
30.97981
ReflectionResolution: 2.5→50 Å / Num. obs: 30088 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→50 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.5 / % possible all: 85.5

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Processing

Software
NameClassification
HKL-2000data collection
SHELXDphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / σ(I): 2
RfactorNum. reflectionSelection details
Rfree0.295 -Random
Rwork0.246 --
obs-24699 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 4 88 6088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009299
X-RAY DIFFRACTIONc_angle_deg1.01753
LS refinement shellResolution: 2.5→50 Å
RfactorNum. reflection% reflection
Rfree0.2954 2243 -
Rwork0.2456 --
obs-29991 82.4 %

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