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- PDB-5hx5: APOBEC3F Catalytic Domain Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 5hx5
TitleAPOBEC3F Catalytic Domain Crystal Structure
ComponentsDNA dC->dU-editing enzyme APOBEC-3F
KeywordsHYDROLASE / APOBEC3F
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / 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 / negative regulation of viral process / cytidine deaminase activity / transposable element silencing ...apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / 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 / negative regulation of viral process / cytidine deaminase activity / transposable element silencing / positive regulation of gene expression via chromosomal CpG island demethylation / negative regulation of viral genome replication / positive regulation of defense response to virus by host / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Activation-induced cytidine deaminase (AID) / APOBEC3, cytosine deaminase domain / : / 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-3F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsShaban, N.M. / Shi, K. / Aihara, H. / Harris, R.S.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure.
Authors: Shaban, N.M. / Shi, K. / Li, M. / Aihara, H. / Harris, R.S.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,8534
Polymers46,7222
Non-polymers1312
Water1,09961
1
A: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,3611
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA dC->dU-editing enzyme APOBEC-3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4262
Polymers23,3611
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.940, 50.900, 100.860
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3F / Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F / A3F


Mass: 23361.082 Da / Num. of mol.: 2 / Fragment: UNP residues 185-373
Mutation: Y196D, H247G, C248R, C259A, F302K, W310D, K355D, K358D, F363D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3F / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IUX4, 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: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.33→35.94 Å / Num. obs: 15324 / % possible obs: 96.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.1173 / Net I/σ(I): 6.1
Reflection shellResolution: 2.33→2.42 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2313: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IOU

4iou


Resolution: 2.33→35.937 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 775 4.74 %
Rwork0.2268 --
obs0.2286 14591 93.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→35.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 2 61 2951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082991
X-RAY DIFFRACTIONf_angle_d0.6024058
X-RAY DIFFRACTIONf_dihedral_angle_d15.9161714
X-RAY DIFFRACTIONf_chiral_restr0.043398
X-RAY DIFFRACTIONf_plane_restr0.005521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.41330.35371400.31962844X-RAY DIFFRACTION97
2.4133-2.50990.39271280.33222815X-RAY DIFFRACTION96
2.5099-2.62410.37631540.32752783X-RAY DIFFRACTION97
2.6241-2.76240.44641360.33922679X-RAY DIFFRACTION91
2.7624-2.93540.29721270.26812814X-RAY DIFFRACTION98
2.9354-3.16190.27831430.24782827X-RAY DIFFRACTION97
3.1619-3.47980.2861270.24812636X-RAY DIFFRACTION90
3.4798-3.98280.28471330.21792468X-RAY DIFFRACTION85
3.9828-5.01570.22251070.16972615X-RAY DIFFRACTION90
5.0157-35.94120.17561550.17532641X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6895-1.07580.3331.743-0.02140.65930.0537-0.12470.61070.438-0.0457-0.4161-0.67880.646-0.00580.3536-0.067-00.513-0.10510.565153.558612.075944.4631
20.1715-0.15290.25640.50470.32660.56130.603-0.16410.1648-0.1539-0.3512-0.2689-0.04780.05830.14880.2572-0.0128-0.06910.436-0.01350.409842.366311.25931.4072
30.98011.08520.60431.75860.1970.56360.31640.1943-0.9871-0.35170.3093-1.1517-0.34970.03180.07580.4312-0.04420.04740.5015-0.07680.362744.11613.481929.1897
41.2599-0.0562.12290.40820.5945.47730.52150.50150.5547-1.1487-1.1113-0.38270.25571.6108-0.24890.7697-0.08840.01060.58060.10940.524241.028420.334926.6967
51.3918-0.0951-0.48581.9138-0.16112.45160.0686-0.00210.0306-0.66730.3191-1.1341-0.9548-0.13080.64570.47870.0246-0.05010.25860.04210.21538.125420.003636.7047
60.53270.1499-0.78391.1505-0.11411.2989-0.4154-0.4710.2905-0.06970.22410.10940.0115-0.85330.2150.43510.158-0.06660.3592-0.0880.418238.62418.012643.707
70.1541-0.2553-0.17380.38310.11660.35140.55350.3210.7301-0.2294-0.64150.3169-0.855-0.11950.00410.443-0.0433-0.02580.4624-0.01930.515233.25823.794347.3219
82.855-1.3689-1.2610.62720.74150.5978-0.60450.0755-0.67220.30020.01160.6474-0.02630.1839-0.43250.27750.0562-0.07610.3989-0.04780.643741.58915.938441.7833
90.20860.52420.28741.36690.35670.59530.02040.20890.30170.30170.3352-0.20.8857-0.27810.29110.24070.0637-0.04710.42710.03620.308253.20070.349743.145
102.6494-1.24130.68241.5898-0.42380.2119-0.7265-0.9452-1.41120.7730.75371.1005-0.4784-0.2382-0.01030.39130.03870.00780.34720.01640.389736.203610.963454.4894
110.0913-0.0942-0.55480.60910.02893.4986-0.1609-0.6619-0.0884-0.1034-1.0447-0.7845-1.27071.5516-0.07840.5840.017-0.00351.24050.22040.723851.0936-5.040214.5632
120.2888-0.39050.35580.81740.06860.60450.44910.63360.4088-0.3043-0.2050.306-0.1253-0.2157-0.0120.62640.03750.09450.5755-0.13530.536831.4717-3.959524.0151
130.02510.2180.24321.0041.14081.10310.42660.1167-0.44371.1089-0.23840.04020.7345-0.33780.00460.71680.0496-0.10420.31590.01120.408739.629-12.411621.3904
141.00920.31331.02191.6189-0.60841.32330.1409-0.46950.1363-0.0617-0.46040.18020.2260.0859-0.29440.25320.00720.08140.4392-0.10060.45733.2026-13.107415.6834
154.5252-0.74380.5641.9895-0.4340.9182-0.0926-0.59850.0884-0.83680.1280.08820.6272-0.0132.11810.65640.14170.08780.2595-0.03860.285134.7597-14.06695.4801
160.53210.631-0.16920.54970.40671.27260.22020.14440.8995-0.1047-0.42490.6627-0.5088-0.1851-0.04270.5255-0.0572-0.00580.37670.02780.435239.5967-0.022710.1644
171.27940.0437-0.82342.4823-0.05261.69460.51610.1062-0.6013-0.9109-0.7127-0.5639-1.08620.9435-0.55541.1162-0.39510.05670.43130.20660.184544.2085-0.04223.9807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 190 through 216 )
2X-RAY DIFFRACTION2chain 'A' and (resid 217 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 249 )
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 267 )
5X-RAY DIFFRACTION5chain 'A' and (resid 268 through 293 )
6X-RAY DIFFRACTION6chain 'A' and (resid 294 through 311 )
7X-RAY DIFFRACTION7chain 'A' and (resid 312 through 323 )
8X-RAY DIFFRACTION8chain 'A' and (resid 324 through 342 )
9X-RAY DIFFRACTION9chain 'A' and (resid 343 through 356 )
10X-RAY DIFFRACTION10chain 'A' and (resid 357 through 373 )
11X-RAY DIFFRACTION11chain 'B' and (resid 190 through 216 )
12X-RAY DIFFRACTION12chain 'B' and (resid 217 through 231 )
13X-RAY DIFFRACTION13chain 'B' and (resid 232 through 261 )
14X-RAY DIFFRACTION14chain 'B' and (resid 262 through 292 )
15X-RAY DIFFRACTION15chain 'B' and (resid 293 through 323 )
16X-RAY DIFFRACTION16chain 'B' and (resid 324 through 342 )
17X-RAY DIFFRACTION17chain 'B' and (resid 343 through 373 )

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