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- PDB-5sxg: Crystal Structure of the Cancer Genomic DNA Mutator APOBEC3B -

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Basic information

Entry
Database: PDB / ID: 5sxg
TitleCrystal Structure of the Cancer Genomic DNA Mutator APOBEC3B
ComponentsDNA dC->dU-editing enzyme APOBEC-3B
KeywordsHYDROLASE / APOBEC / deaminase
Function / homology
Function and homology information


mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : ...mRNA Editing: C to U Conversion / Formation of the Editosome / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / retrotransposon silencing / P-body / defense response to virus / innate immune response / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
APOBEC-like C-terminal domain / 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
IMIDAZOLE / 1,3-PROPANDIOL / DNA dC->dU-editing enzyme APOBEC-3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsShi, K. / Kurahashi, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095558 and GM109770 United States
CitationJournal: Sci Rep / Year: 2017
Title: Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B.
Authors: Shi, K. / Demir, O. / Carpenter, M.A. / Wagner, J. / Kurahashi, K. / Harris, R.S. / Amaro, R.E. / Aihara, H.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / 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 / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _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-3B
B: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,30011
Polymers43,6432
Non-polymers6569
Water5,062281
1
A: DNA dC->dU-editing enzyme APOBEC-3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1085
Polymers21,8221
Non-polymers2874
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)22,1916
Polymers21,8221
Non-polymers3705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.390, 50.800, 76.890
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3B / A3B / Phorbolin-1-related protein / Phorbolin-2/3


Mass: 21821.688 Da / Num. of mol.: 2 / Mutation: F200S, W228S, L230K, Y250S, F308K, Delta 242-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3B / Production host: Escherichia coli (E. coli)
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: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350

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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: Dec 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 25238 / % possible obs: 99.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10.2
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.549 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIXdev_2499refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQK

5cqk


Resolution: 1.93→37.481 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1217 4.83 %
Rwork0.1766 --
obs0.1783 25220 99.73 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→37.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 37 281 3202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063001
X-RAY DIFFRACTIONf_angle_d0.674054
X-RAY DIFFRACTIONf_dihedral_angle_d18.2621757
X-RAY DIFFRACTIONf_chiral_restr0.047410
X-RAY DIFFRACTIONf_plane_restr0.004526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9301-2.00740.28521410.2712596X-RAY DIFFRACTION99
2.0074-2.09870.27681300.23612651X-RAY DIFFRACTION100
2.0987-2.20940.24391360.21612647X-RAY DIFFRACTION100
2.2094-2.34780.23391460.20182647X-RAY DIFFRACTION100
2.3478-2.5290.24661150.1872660X-RAY DIFFRACTION100
2.529-2.78340.21051380.17922696X-RAY DIFFRACTION100
2.7834-3.1860.21021430.17042666X-RAY DIFFRACTION100
3.186-4.01330.18431290.14272693X-RAY DIFFRACTION100
4.0133-37.48770.17261390.15362747X-RAY DIFFRACTION100
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)
10.0715-0.0568-0.02170.05740.06490.1388-0.04620.0013-0.10850.06010.08990.1322-0.057-0.05280.00990.1473-0.0170.04050.1646-0.01250.2202-1.2667-0.0243-3.7543
20.17160.10860.18740.23490.17690.3722-0.14510.1012-0.00660.10170.1075-0.1354-0.0116-0.1242-0.00010.20260.0020.01320.2088-0.00530.18392.86973.2644.6841
30.18460.05120.16010.2015-0.09740.21990.05970.001-0.0353-0.07370.1450.01-0.01520.0330.01470.1912-0.00230.00590.1945-0.01940.234511.56171.5631-1.9956
40.2450.23120.10630.21630.15110.2979-0.08670.1052-0.0476-0.07150.0886-0.11690.0141-0.0757-0.01860.1549-0.02420.01050.1415-0.00110.23917.0967.2859-2.5804
50.5229-0.1980.41070.1092-0.19080.3411-0.10440.0496-0.10610.09810.0588-0.1157-0.0841-0.0389-0.02960.1614-0.001-0.03960.16960.03860.186913.12937.08039.8505
60.14350.00090.00090.06940.07540.1534-0.0656-0.0534-0.08190.04870.0246-0.1809-0.1131-0.0527-0.00180.1946-0.0048-0.05840.15790.00780.211210.290712.937812.8922
70.2315-0.1874-0.09570.14810.07380.03740.01370.0034-0.1367-0.0672-0.05390.0003-0.0777-0.0236-00.16580.0196-0.02550.1783-0.0090.177-5.97888.1862-4.2462
80.07710.1268-0.07770.2825-0.18590.1532-0.12540.10580.04130.11870.01860.2086-0.19390.0782-0.00070.18530.047-0.02970.2112-0.0120.1515-1.461915.309213.8861
90.00160.0071-0.01150.0746-0.00320.05350.23610.06720.02520.0452-0.1123-0.03760.10810.09040.00040.25890.00990.02710.20120.0290.186937.9763-6.04940.9383
100.7169-0.47480.40450.7866-0.40920.50660.165-0.1079-0.0549-0.0451-0.02410.05970.0385-0.08460.29670.17440.00980.03550.15220.01620.144327.096-4.062637.5615
110.69090.330.37010.23890.00120.545-0.024-0.0044-0.03520.04350.13320.1947-0.1845-0.15650.13930.19820.07090.04390.25910.04640.204219.14361.837636.117
120.84890.42170.17630.80380.32070.1309-0.221-0.2812-0.05460.22170.23720.1651-0.1125-0.23820.22250.18720.10720.03070.30550.05190.14318.58597.035137.972
130.12260.08310.17641.0082-0.42610.32190.0904-0.00050.0109-0.0096-0.160.0189-0.0082-0.0104-0.00280.2270.031-0.00170.21350.00450.158533.82574.508330.926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 190 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 279 )
5X-RAY DIFFRACTION5chain 'A' and (resid 280 through 318 )
6X-RAY DIFFRACTION6chain 'A' and (resid 319 through 337 )
7X-RAY DIFFRACTION7chain 'A' and (resid 338 through 361 )
8X-RAY DIFFRACTION8chain 'A' and (resid 362 through 378 )
9X-RAY DIFFRACTION9chain 'B' and (resid 190 through 202 )
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 265 )
11X-RAY DIFFRACTION11chain 'B' and (resid 266 through 298 )
12X-RAY DIFFRACTION12chain 'B' and (resid 299 through 309 )
13X-RAY DIFFRACTION13chain 'B' and (resid 310 through 378 )

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