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- PDB-5tkm: Crystal structure of human APOBEC3B N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5tkm
TitleCrystal structure of human APOBEC3B N-terminal Domain
ComponentsDNA dC->dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE / DEAMINASE / APOBEC
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element silencing / P-body ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / DNA cytosine deamination / cytidine to uridine editing / clearance of foreign intracellular DNA / cytidine deaminase activity / transposable element silencing / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Novel AID APOBEC clade 2 / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsXiao, X. / Yang, H. / Arutiunian, V. / Besse, G. / Morimoto, C. / Zirkle, B. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087986 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation.
Authors: Xiao, X. / Yang, H. / Arutiunian, V. / Fang, Y. / Besse, G. / Morimoto, C. / Zirkle, B. / Chen, X.S.
History
DepositionOct 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / pdbx_audit_support / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3B
B: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2984
Polymers47,1672
Non-polymers1312
Water4,216234
1
A: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6492
Polymers23,5841
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6492
Polymers23,5841
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.739, 60.802, 111.515
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 DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 23583.730 Da / Num. of mol.: 2 / Mutation: Y13D, Y28S, Y83D, W127S, Y146K, Y162D, Y191H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q9UH17, 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.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01 M Iron (III) chloride hexahydrate, 0.1 M sodium citrate dehydrate pH 5.6, 10% v/v Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33189 / % possible obs: 99.8 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.19

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K81

5k81


Resolution: 1.9→30.37 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.59
RfactorNum. reflection% reflection
Rfree0.2027 1993 6.02 %
Rwork0.1877 --
obs0.1886 33127 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 2 234 3368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073234
X-RAY DIFFRACTIONf_angle_d0.7934382
X-RAY DIFFRACTIONf_dihedral_angle_d15.4281174
X-RAY DIFFRACTIONf_chiral_restr0.053428
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8997-1.94720.29021350.23942098X-RAY DIFFRACTION97
1.9472-1.99980.26611440.22632212X-RAY DIFFRACTION100
1.9998-2.05860.23671400.21142183X-RAY DIFFRACTION100
2.0586-2.12510.251370.21632204X-RAY DIFFRACTION100
2.1251-2.2010.23771420.21442223X-RAY DIFFRACTION100
2.201-2.28910.24671380.1972187X-RAY DIFFRACTION100
2.2891-2.39320.22941420.20522221X-RAY DIFFRACTION100
2.3932-2.51930.18331470.20852213X-RAY DIFFRACTION100
2.5193-2.67710.21731420.1972229X-RAY DIFFRACTION100
2.6771-2.88360.19341410.19882263X-RAY DIFFRACTION100
2.8836-3.17360.17911430.18322230X-RAY DIFFRACTION100
3.1736-3.63210.19311410.17252246X-RAY DIFFRACTION100
3.6321-4.57360.17471500.15382283X-RAY DIFFRACTION100
4.5736-30.37340.2041510.19272342X-RAY DIFFRACTION97

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