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- PDB-1e9n: A second divalent metal ion in the active site of a new crystal f... -

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Basic information

Entry
Database: PDB / ID: 1e9n
TitleA second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism
ComponentsDNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
KeywordsDNA REPAIR / DNA REPAIR ENDONUCLEASE / BASE EXCISION REPAIR / ABASIC ENDONUCLEASE / APE1 / HAP1 / REF-1 / ALPHA / BETA SANDWICH
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
LEAD (II) ION / DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBeernink, P.T. / Segelke, B.W. / Rupp, B.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
Authors: Beernink, P.T. / Segelke, B.W. / Hadi, M.Z. / Erzberger, J.P. / Wilson III, D.M. / Rupp, B.
History
DepositionOct 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
B: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0426
Polymers71,2132
Non-polymers8294
Water6,287349
1
A: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0213
Polymers35,6061
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0213
Polymers35,6061
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)137.522, 45.016, 125.702
Angle α, β, γ (deg.)90.00, 108.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.979, -0.046, -0.198), (-0.046, 0.999, -0.004), (0.198, 0.005, -0.98)27.189, 0.6263, 27.3501
2given(-0.989, -0.005, -0.149), (-0.006, 1, 0.003), (0.149, 0.003, -0.989)26.9468, 0.0301, 27.9127
DetailsTHE BIOLOGICAL UNIT IS HALF OF THE ASYMMETRIC UNIT

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Components

#1: Protein DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE / AP ENDONUCLEASE 1 / HAP1 / REF1 / APE1


Mass: 35606.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: APE1 / Plasmid: PET11D / Gene (production host): APE1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDONUCLEOLYTIC CLEAVAGE NEAR APURINIC OR APYRIMIDINIC SITES TO PRODUCTS WITH 5'-PHOSPHATE.
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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
30.2 Msodium acetate1reservoir
425 %PEG40001reservoir
51 mMlead (II) acetate1reservoir
619.5 mMHECAMEG1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.2398
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 1999 / Details: DUAL CRYSTAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 2.2→67.42 Å / Num. obs: 34905 / % possible obs: 93 % / Redundancy: 2.9 % / Rsym value: 0.082 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.1 / % possible all: 70.5
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 102875 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 70.5 %

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Processing

Software
NameVersionClassification
TNT5Frefinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TO BE PUBLISHED

Resolution: 2.2→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO_V012 / Details: NCS WEIGHT 60, THEN RELAXED AT END OF REFINEMENT
RfactorNum. reflection% reflection
Rfree0.252 -10 %
Rwork0.186 --
all-34905 -
obs-31342 93 %
Solvent computationSolvent model: BABENET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 4 349 4689
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01844500.6
X-RAY DIFFRACTIONt_angle_deg2.3259971.8
X-RAY DIFFRACTIONt_dihedral_angle_d18.9226070
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0071052
X-RAY DIFFRACTIONt_gen_planes0.0166425
X-RAY DIFFRACTIONt_it3.244502
X-RAY DIFFRACTIONt_nbd0.2285010
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 3499 / Rfactor all: 0.186 / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.920
X-RAY DIFFRACTIONt_planar_d0.0072
X-RAY DIFFRACTIONt_plane_restr0.0165

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