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- PDB-4lnd: Crystal structure of human apurinic/apyrimidinic endonuclease 1 w... -

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Basic information

Entry
Database: PDB / ID: 4lnd
TitleCrystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor
ComponentsDNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE / apurinic/apyrimidinic endonuclease
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III ...Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / phosphodiesterase I activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / regulation of mRNA stability / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / RNA-DNA hybrid ribonuclease activity / transcription corepressor activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / nuclear speck / ribosome / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase ...AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsManvilla, B.A. / Pozharski, E. / Toth, E.A. / Drohat, A.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg(2+) cofactor.
Authors: Manvilla, B.A. / Pozharski, E. / Toth, E.A. / Drohat, A.C.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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

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Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase
C: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3746
Polymers96,3013
Non-polymers733
Water2,162120
1
A: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1252
Polymers32,1001
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1252
Polymers32,1001
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1252
Polymers32,1001
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.795, 90.940, 94.030
Angle α, β, γ (deg.)90.00, 123.22, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.800426, 0.321267, 0.506068), (0.299419, -0.517097, 0.801847), (0.519293, 0.793346, 0.317704)22.54366, -96.19858, 49.71239
3given(0.819801, -0.159941, -0.549859), (0.391941, -0.543342, 0.742403), (-0.417502, -0.824135, -0.382745)14.43049, -53.45805, 24.64984

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) lyase / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / AP endonuclease 1 / APE-1 / REF-1 / ...APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / AP endonuclease 1 / APE-1 / REF-1 / Redox factor-1 / DNA-(apurinic or apyrimidinic site) lyase / mitochondrial


Mass: 32100.492 Da / Num. of mol.: 3 / Fragment: UNP residues 39-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APE, APE1, APEX, APEX1, APX, HAP1, REF1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.03325 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2012
RadiationMonochromator: Side scattering I-beam bent single Si(111) crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03325 Å / Relative weight: 1
ReflectionResolution: 1.92→69.35 Å / Num. all: 75632 / Num. obs: 75632 / % possible obs: 85.4 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.6
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 0.7 / % possible all: 84.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BIX

1bix


Resolution: 1.92→48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.091 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24052 3746 5 %RANDOM
Rwork0.21734 ---
obs0.2185 71263 84.38 %-
all-75632 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.649 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.91 Å2
2---0.25 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.92→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6331 0 3 120 6454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196493
X-RAY DIFFRACTIONr_bond_other_d0.0010.025925
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9678867
X-RAY DIFFRACTIONr_angle_other_deg3.37313604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47223.656279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4915964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71538
X-RAY DIFFRACTIONr_chiral_restr0.0710.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217459
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021495
X-RAY DIFFRACTIONr_mcbond_it0.7832.2373297
X-RAY DIFFRACTIONr_mcbond_other0.7832.2373296
X-RAY DIFFRACTIONr_mcangle_it1.2953.3514116
X-RAY DIFFRACTIONr_mcangle_other1.2943.3514117
X-RAY DIFFRACTIONr_scbond_it0.732.2783196
X-RAY DIFFRACTIONr_scbond_other0.732.2783196
X-RAY DIFFRACTIONr_scangle_other1.213.394751
X-RAY DIFFRACTIONr_long_range_B_refined2.84618.0677188
X-RAY DIFFRACTIONr_long_range_B_other2.84118.0127161
LS refinement shellResolution: 1.922→1.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 265 -
Rwork0.293 5272 -
obs--84.25 %
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)
13.8661-4.0206-0.403612.30471.63651.7639-0.21-0.5563-0.09290.75260.2279-0.0452-0.12860.2889-0.01790.1593-0.035-0.05670.21940.06440.072945.3364-32.240354.6492
22.1149-1.96520.85973.4176-1.48641.53770.11280.02760.2037-0.0482-0.0778-0.3256-0.18360.2723-0.0350.1022-0.03750.01850.16930.020.134745.363-24.303135.7803
33.9339-2.2168-1.95722.30360.51371.31440.45640.27220.3827-0.3624-0.383-0.4542-0.14630.055-0.07340.24390.015-0.0110.43890.0120.234549.0383-26.398326.3899
41.5272-0.0043-0.29340.9194-0.15721.33380.04520.0989-0.13970.0585-0.00760.07510.0140.0282-0.03760.0243-0.0101-0.01290.03920.01770.048733.5111-32.890338.6229
57.1916-4.07913.19454.8429-2.6475.27230.0033-0.42270.6590.3894-0.1081-0.1349-0.37860.09840.10480.287-0.00850.0610.0969-0.06570.25343.6546-21.807564.2503
62.3284-1.48310.29553.2448-0.04011.48980.0228-0.357-0.12480.0881-0.00380.21420.0444-0.2521-0.0190.084-0.00760.05540.1199-0.00530.0758-4.1766-41.106164.8774
72.7486-1.5796-0.30170.96580.44671.9186-0.0051-0.2813-0.35880.02690.07560.24430.1231-0.2924-0.07050.1683-0.03350.06280.1859-0.01830.2306-12.0879-45.809662.5134
81.52860.3010.01160.8772-0.02051.16380.0208-0.0248-0.062-0.0806-0.0929-0.068-0.0359-0.00570.07210.09450.01560.04550.01210.00350.05784.5994-38.103152.9373
92.58050.2178-2.38525.8411-6.354211.26490.02260.3142-0.5371-0.70420.02820.0721.0979-0.0357-0.05080.191-0.0058-0.06850.1939-0.14290.198621.1206-41.1476-12.7451
101.1406-0.409-0.4580.79410.3684.5180.0209-0.0162-0.13060.0699-0.1027-0.09680.05140.35750.08180.062-0.0165-0.00570.1685-0.03420.088532.5445-30.24650.4972
111.0252-0.7552-0.13181.7343-0.43341.92260.07760.07470.2129-0.1296-0.0474-0.3215-0.26420.5109-0.03020.1443-0.05260.0230.2135-0.06760.159738.1196-21.68310.5429
122.0902-0.0679-0.0731.4991-0.16551.34480.1071-0.0039-0.0157-0.0286-0.04270.1612-0.0653-0.2288-0.06430.0390.00060.00060.153-0.0660.063917.7741-25.6927-0.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 59
2X-RAY DIFFRACTION2A60 - 99
3X-RAY DIFFRACTION3A101 - 122
4X-RAY DIFFRACTION4A123 - 318
5X-RAY DIFFRACTION5B44 - 59
6X-RAY DIFFRACTION6B60 - 100
7X-RAY DIFFRACTION7B102 - 122
8X-RAY DIFFRACTION8B123 - 318
9X-RAY DIFFRACTION9C44 - 59
10X-RAY DIFFRACTION10C60 - 99
11X-RAY DIFFRACTION11C100 - 122
12X-RAY DIFFRACTION12C123 - 318

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