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- PDB-5cfe: Bacillus subtilis AP endonuclease ExoA -

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Basic information

Entry
Database: PDB / ID: 5cfe
TitleBacillus subtilis AP endonuclease ExoA
ComponentsExodeoxyribonuclease
KeywordsHYDROLASE / AP endonuclease
Function / homology
Function and homology information


: / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA binding / metal ion binding / 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
DI(HYDROXYETHYL)ETHER / Exodeoxyribonuclease
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMorera, S. / Vigouroux, A.
CitationJournal: Biochimie / Year: 2016
Title: Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA.
Authors: Redrejo-Rodriguez, M. / Vigouroux, A. / Mursalimov, A. / Grin, I. / Alili, D. / Koshenov, Z. / Akishev, Z. / Maksimenko, A. / Bissenbaev, A.K. / Matkarimov, B.T. / Saparbaev, M. / Ishchenko, A.A. / Morera, S.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7237
Polymers29,2841
Non-polymers4396
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-9 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.280, 61.920, 73.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exodeoxyribonuclease


Mass: 29283.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: exoA, BSU40880 / Production host: Escherichia coli (E. coli) / References: UniProt: P37454, exodeoxyribonuclease III
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 16% (w/v) PEG 4000, 0.2 M CaCl2, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2011
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→40 Å / Num. obs: 21097 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.09 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.09
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.99 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BIX

1bix


Resolution: 1.84→42.57 Å / Cor.coef. Fo:Fc: 0.9523 / Cor.coef. Fo:Fc free: 0.9254 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1055 5 %RANDOM
Rwork0.1671 ---
obs0.1691 21096 99.14 %-
Displacement parametersBiso mean: 21.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.4694 Å20 Å20 Å2
2---0.5691 Å20 Å2
3---0.0997 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.84→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 24 189 2275
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092126HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072868HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d759SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes300HARMONIC5
X-RAY DIFFRACTIONt_it2126HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.9
X-RAY DIFFRACTIONt_other_torsion19.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
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_contact2654SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.93 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2278 133 5 %
Rwork0.1969 2529 -
all0.1985 2662 -
obs--99.14 %
Refinement TLS params.Method: refined / Origin x: -24.1666 Å / Origin y: 1.7243 Å / Origin z: -1.1375 Å
111213212223313233
T-0.0307 Å20.0117 Å20.0029 Å2--0.0662 Å2-0.0046 Å2---0.0325 Å2
L1.023 °20.0242 °20.5352 °2-0.7542 °2-0.1293 °2--1.0622 °2
S0.0897 Å °0.0363 Å °-0.0591 Å °-0.0179 Å °-0.0428 Å °-0.0048 Å °0.1122 Å °0.0249 Å °-0.0468 Å °
Refinement TLS groupSelection details: { A|* }

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