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- PDB-2jc4: 3'-5' exonuclease (NExo) from Neisseria Meningitidis -

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Basic information

Entry
Database: PDB / ID: 2jc4
Title3'-5' exonuclease (NExo) from Neisseria Meningitidis
ComponentsEXODEOXYRIBONUCLEASE III
KeywordsHYDROLASE / NEISSERIA MENINGITIDIS / REPAIR PHOSPHODIESTERASE / DNA REPAIR / EXONUCLEASE / ENDONUCLEASE
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / endonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / 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 ...Exodeoxyribonuclease III-like / 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
DIHYDROGENPHOSPHATE ION / ACETATE ION / Exodeoxyribonuclease III
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCarpenter, E.P. / Corbett, A. / Thomson, H. / Adacha, J. / Jensen, K. / Bergeron, J. / Kasampalidis, I. / Exley, R. / Winterbotham, M. / Tang, C. ...Carpenter, E.P. / Corbett, A. / Thomson, H. / Adacha, J. / Jensen, K. / Bergeron, J. / Kasampalidis, I. / Exley, R. / Winterbotham, M. / Tang, C. / Baldwin, G. / Freemont, P.
CitationJournal: Embo J. / Year: 2007
Title: Ap Endonuclease Paralogues with Distinct Activities in DNA Repair and Bacterial Pathogenesis.
Authors: Carpenter, E.P. / Corbett, A. / Thomson, H. / Adacha, J. / Jensen, K. / Bergeron, J. / Kasampalidis, I. / Exley, R. / Winterbotham, M. / Tang, C. / Baldwin, G.S. / Freemont, P.
History
DepositionDec 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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.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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXODEOXYRIBONUCLEASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6557
Polymers29,1901
Non-polymers4656
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.193, 58.618, 88.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein EXODEOXYRIBONUCLEASE III / NEISSERIA MENINGITIDIS 3'-5' EXONUCLEASE-NEXO


Mass: 29190.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: MC58 SEROGROUP B / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9K100, exodeoxyribonuclease III

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Non-polymers , 6 types, 293 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 31.3 %
Crystal growpH: 6.5
Details: PROTEIN CONCENTRATION 8.7MG/ML BUFFER: 10 MM TRIS, PH 7.0, 100 MM NACL . WELL SOLUTION: 100 MM NA CACODYLATE PH 6 200 MM NA ACETATE, 15 % PEG 8000. THE CRYSTALLISATION PLATES USED WERE ...Details: PROTEIN CONCENTRATION 8.7MG/ML BUFFER: 10 MM TRIS, PH 7.0, 100 MM NACL . WELL SOLUTION: 100 MM NA CACODYLATE PH 6 200 MM NA ACETATE, 15 % PEG 8000. THE CRYSTALLISATION PLATES USED WERE CORNING ROUND BOTTOM 96 WELL PLATES. THE CRYSTALLISATION DROPS CONSISTED OF 1UL PROTEIN AND 1UL WELL SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 19164 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.5
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BIX

1bix


Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.953 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.FIVE RESIDUES HAVE UNUSUAL PHI PSI VALUES. THESE ARE RESIDUES SER 10, THR 61, ASN 63, GLU 110 AND HIS 167. THESE RESIDUES FIT THE ELECTRON ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.FIVE RESIDUES HAVE UNUSUAL PHI PSI VALUES. THESE ARE RESIDUES SER 10, THR 61, ASN 63, GLU 110 AND HIS 167. THESE RESIDUES FIT THE ELECTRON DENSITY WELL IN OMIT MAPS AND THEY ARE THOUGHT TO BE THE RESULT OF USUAL BACKBONE CONFORMATIONS. RESIDUES CYS 156 AND CYS 168 FORM A PARTIAL DISULPHIDE BRIDGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 982 5.18 %RAMDOM
Rwork0.152 ---
obs-19112 100 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.193 Å20 Å20 Å2
2--0.079 Å20 Å2
3----0.272 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 28 287 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9542947
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93824.175103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59415344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1771514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021669
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21043
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21453
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7831.51318
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37222133
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3283882
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.54.5811
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7.85→19.96 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 13
Rwork0.195 282

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