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- PDB-6khy: The crystal structure of AsfvAP:AG -

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Basic information

Entry
Database: PDB / ID: 6khy
TitleThe crystal structure of AsfvAP:AG
Components
  • DNA (AGCGTCACCGACGAGGC)
  • DNA(AGCGTCACCGACGAGG)
  • DNA(CCTCGTCGGGGACGC)
  • DNA(CCTCGTCGGGGACGCT)
  • DNA(CCTCGTCGGGGACGCTG)
  • DNA(GCAGCGTCACCGACGAGG)
  • Probable AP endonuclease
KeywordsDNA BINDING PROTEIN / EndonucleaseIV / ASFV
Function / homology
Function and homology information


phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / virion component / endonuclease activity / host cell cytoplasm / host cell nucleus / DNA binding / zinc ion binding
Similarity search - Function
AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease family 2 / AP endonuclease 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel ...AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease family 2 / AP endonuclease 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Probable AP endonuclease
Similarity search - Component
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.008 Å
AuthorsChen, Y.Q. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Cell Discov / Year: 2020
Title: A unique DNA-binding mode of African swine fever virus AP endonuclease.
Authors: Chen, Y. / Chen, X. / Huang, Q. / Shao, Z. / Gao, Y. / Li, Y. / Yang, C. / Liu, H. / Li, J. / Wang, Q. / Ma, J. / Zhang, Y.Z. / Gu, Y. / Gan, J.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable AP endonuclease
B: Probable AP endonuclease
C: Probable AP endonuclease
D: Probable AP endonuclease
E: DNA(CCTCGTCGGGGACGCTG)
F: DNA(GCAGCGTCACCGACGAGG)
G: DNA(CCTCGTCGGGGACGCT)
H: DNA(AGCGTCACCGACGAGG)
I: DNA(CCTCGTCGGGGACGC)
J: DNA (AGCGTCACCGACGAGGC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,01126
Polymers165,44510
Non-polymers1,56616
Water00
1
A: Probable AP endonuclease
C: Probable AP endonuclease
E: DNA(CCTCGTCGGGGACGCTG)
F: DNA(GCAGCGTCACCGACGAGG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,58112
Polymers77,7984
Non-polymers7838
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable AP endonuclease
G: DNA(CCTCGTCGGGGACGCT)
H: DNA(AGCGTCACCGACGAGG)
hetero molecules

B: Probable AP endonuclease
G: DNA(CCTCGTCGGGGACGCT)
H: DNA(AGCGTCACCGACGAGG)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,11614
Polymers87,3336
Non-polymers7838
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
3
D: Probable AP endonuclease
I: DNA(CCTCGTCGGGGACGC)
J: DNA (AGCGTCACCGACGAGGC)
hetero molecules

D: Probable AP endonuclease
I: DNA(CCTCGTCGGGGACGC)
J: DNA (AGCGTCACCGACGAGGC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,74414
Polymers87,9616
Non-polymers7838
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)110.512, 148.504, 178.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain I and (resseq 2:3 or resseq 5:7 or resseq 9:16))
21(chain G and (resseq 2:3 or resseq 5:7 or resseq 9:16))
12(chain A and (resseq -2:7 or resseq 10:16 or (resid...
22(chain B and (resseq -2:7 or resseq 10:13 or (resid...
32(chain C and (resseq -2:7 or resseq 10:13 or (resid...
42(chain D and (resseq -2:7 or resseq 10:16 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label alt-IDBeg label comp-IDEnd auth comp-IDEnd label alt-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DCADCDCADC(chain I and (resseq 2:3 or resseq 5:7 or resseq 9:16))II2 - 32 - 3
121DCADCDTADT(chain I and (resseq 2:3 or resseq 5:7 or resseq 9:16))II5 - 75 - 7
131DGADGDCADC(chain I and (resseq 2:3 or resseq 5:7 or resseq 9:16))II9 - 169 - 16
211DCBDCDCBDC(chain G and (resseq 2:3 or resseq 5:7 or resseq 9:16))GG2 - 31 - 2
221DCBDCDTBDT(chain G and (resseq 2:3 or resseq 5:7 or resseq 9:16))GG5 - 74 - 6
231DGBDGDCBDC(chain G and (resseq 2:3 or resseq 5:7 or resseq 9:16))GG9 - 168 - 15
112GLYGLYSERSER(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA-2 - 73 - 12
122LEULEUCYSCYS(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA10 - 1615 - 21
132GLYGLYGLYGLY(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA05
142GLYGLYLYSLYS(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA-2 - 2963 - 301
152GLYGLYLYSLYS(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA-2 - 2963 - 301
162GLYGLYLYSLYS(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA-2 - 2963 - 301
172GLYGLYLYSLYS(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA-2 - 2963 - 301
182GLYGLYLYSLYS(chain A and (resseq -2:7 or resseq 10:16 or (resid...AA-2 - 2963 - 301
212GLYGLYSERSER(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB-2 - 73 - 12
222LEULEUASPASP(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB10 - 1315 - 18
232SERSERSERSER(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB1419
242GLYGLYLYSLYS(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB-2 - 2963 - 301
252GLYGLYLYSLYS(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB-2 - 2963 - 301
262GLYGLYLYSLYS(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB-2 - 2963 - 301
272GLYGLYLYSLYS(chain B and (resseq -2:7 or resseq 10:13 or (resid...BB-2 - 2963 - 301
312GLYGLYSERSER(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC-2 - 73 - 12
322LEULEUASPASP(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC10 - 1315 - 18
332GLYGLYGLYGLY(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC05
342GLYGLYLYSLYS(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC-2 - 2963 - 301
352GLYGLYLYSLYS(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC-2 - 2963 - 301
362GLYGLYLYSLYS(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC-2 - 2963 - 301
372GLYGLYLYSLYS(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC-2 - 2963 - 301
382GLYGLYLYSLYS(chain C and (resseq -2:7 or resseq 10:13 or (resid...CC-2 - 2963 - 301
412GLYGLYSERSER(chain D and (resseq -2:7 or resseq 10:16 or (resid...DD-2 - 73 - 12
422LEULEUCYSCYS(chain D and (resseq -2:7 or resseq 10:16 or (resid...DD10 - 1615 - 21
432THRTHRTHRTHR(chain D and (resseq -2:7 or resseq 10:16 or (resid...DD1722

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Probable AP endonuclease / APE


Mass: 33842.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus (isolate Tick/South Africa/Pretoriuskop Pr4/1996)
Strain: isolate Tick/South Africa/Pretoriuskop Pr4/1996 / Gene: Pret-146 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0C9C6, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters

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DNA chain , 6 types, 6 molecules EFGHIJ

#2: DNA chain DNA(CCTCGTCGGGGACGCTG)


Mass: 5220.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) African swine fever virus
#3: DNA chain DNA(GCAGCGTCACCGACGAGG)


Mass: 4893.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) African swine fever virus
#4: DNA chain DNA(CCTCGTCGGGGACGCT)


Mass: 4891.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) African swine fever virus
#5: DNA chain DNA(AGCGTCACCGACGAGG)


Mass: 4933.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) African swine fever virus
#6: DNA chain DNA(CCTCGTCGGGGACGC)


Mass: 4916.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) African swine fever virus
#7: DNA chain DNA (AGCGTCACCGACGAGGC)


Mass: 5222.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) African swine fever virus

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Non-polymers , 2 types, 16 molecules

#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 16% w/v PEG 3350 0.1 M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 28960 / % possible obs: 98.3 % / Redundancy: 7.5 % / Biso Wilson estimate: 60.14 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.031 / Rrim(I) all: 0.091 / Χ2: 0.669 / Net I/σ(I): 6.7 / Num. measured all: 215889
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.114.50.36227710.6210.1750.4050.28296
3.11-3.234.90.31928220.8280.1470.3540.32196.5
3.23-3.385.40.25628290.9180.110.280.32897.5
3.38-3.565.50.23328720.6320.10.2550.59597.9
3.56-3.786.30.16628560.7250.0680.180.49598.4
3.78-4.0780.12529040.9930.0440.1330.54599.2
4.07-4.489.10.08629150.9980.0280.0910.62299.5
4.48-5.129.70.07229650.9990.0230.0760.70499.7
5.12-6.449.80.06629560.9990.0210.0690.76999.4
6.44-3010.70.04330700.9990.0130.0451.19599.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 3.008→29.934 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 25.99
RfactorNum. reflection% reflection
Rfree0.2492 1461 5.06 %
Rwork0.2106 --
obs0.2125 28896 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 185.7 Å2 / Biso mean: 55.875 Å2 / Biso min: 11.67 Å2
Refinement stepCycle: final / Resolution: 3.008→29.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9209 2002 32 0 11243
Biso mean--53.34 --
Num. residues----1290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311701
X-RAY DIFFRACTIONf_angle_d0.55416316
X-RAY DIFFRACTIONf_chiral_restr0.0411864
X-RAY DIFFRACTIONf_plane_restr0.0031705
X-RAY DIFFRACTIONf_dihedral_angle_d20.1126456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11I242X-RAY DIFFRACTION10.599TORSIONAL
12G242X-RAY DIFFRACTION10.599TORSIONAL
21A5108X-RAY DIFFRACTION10.599TORSIONAL
22B5108X-RAY DIFFRACTION10.599TORSIONAL
23C5108X-RAY DIFFRACTION10.599TORSIONAL
24D5108X-RAY DIFFRACTION10.599TORSIONAL
LS refinement shellResolution: 3.0082→3.1156 Å
RfactorNum. reflection
Rfree0.3436 161
Rwork0.3084 -
obs-2610

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