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- PDB-2o3c: Crystal structure of zebrafish Ape -

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Basic information

Entry
Database: PDB / ID: 2o3c
TitleCrystal structure of zebrafish Ape
ComponentsAPEX nuclease 1
KeywordsDNA BINDING PROTEIN / APE / ENDONUCLEASE
Function / homology
Function and homology information


Displacement of DNA glycosylase by APEX1 / POLB-Dependent Long Patch Base Excision Repair / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / : / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / Resolution of Abasic Sites (AP sites) / : / phosphodiesterase I activity / : / double-stranded DNA 3'-5' DNA exonuclease activity ...Displacement of DNA glycosylase by APEX1 / POLB-Dependent Long Patch Base Excision Repair / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / : / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / Resolution of Abasic Sites (AP sites) / : / phosphodiesterase I activity / : / double-stranded DNA 3'-5' DNA exonuclease activity / heart contraction / heart looping / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / Hydrolases; Acting on ester bonds / nuclear speck / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / DNA binding / RNA binding / metal ion binding / nucleus
Similarity search - Function
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 ...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-(apurinic or apyrimidinic site) endonuclease / DNA-(apurinic or apyrimidinic site) endonuclease
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGeorgiadis, M.M. / Gaur, R.K. / Delaplane, S. / Svenson, J.
CitationJournal: Mutat.Res. / Year: 2008
Title: Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease
Authors: Georgiadis, M.M. / Luo, M. / Gaur, R.K. / Delaplane, S. / Li, X. / Kelley, M.R.
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: APEX nuclease 1
B: APEX nuclease 1
C: APEX nuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4786
Polymers95,8573
Non-polymers6223
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.660, 117.780, 85.840
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APEX nuclease 1 / Apurinic/apyrimidinic endonuclease


Mass: 31952.279 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: apex1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ROSETTA / References: UniProt: Q7SXL6, UniProt: A0MTA1*PLUS
#2: Chemical ChemComp-PB / LEAD (II) ION / Lead


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


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.8 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: AMMONIUM ACETATE, BIS-TRIS, PEG 3350, GLYCEROL, LEAD ACETATE, PH 5.5, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 22, 2005
RadiationMonochromator: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 47731 / Num. obs: 46075 / % possible obs: 96.5 % / Redundancy: 3.07 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.4 / % possible all: 85.5

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
JBluIce-EPICSGUI/ BLUE ICEdata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BIX

1bix


Resolution: 2.3→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2294 4.8 %RANDOM
Rwork0.199 ---
obs0.199 46050 96.5 %-
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.751 Å20 Å22.615 Å2
2--0.703 Å20 Å2
3---1.048 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.268 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.267 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 3 362 7009
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_mcbond_it1.3531.5
X-RAY DIFFRACTIONc_mcangle_it2.2422
X-RAY DIFFRACTIONc_scbond_it1.9362
X-RAY DIFFRACTIONc_scangle_it2.8092.5
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.319 277 -
Rwork0.276 --
obs-5202 85.5 %

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