+Open data
-Basic information
Entry | Database: PDB / ID: 2jc4 | ||||||
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Title | 3'-5' exonuclease (NExo) from Neisseria Meningitidis | ||||||
Components | EXODEOXYRIBONUCLEASE III | ||||||
Keywords | HYDROLASE / 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 | ||||||
Biological species | NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Carpenter, 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. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jc4.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jc4.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jc4_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 2jc4_full_validation.pdf.gz | 453.3 KB | Display | |
Data in XML | 2jc4_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 2jc4_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jc4 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jc4 | HTTPS FTP |
-Related structure data
Related structure data | 2jc5C 1bixS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-1PE / | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-2HP / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 31.3 % |
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Crystal grow | pH: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.96 Å
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