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Yorodumi- PDB-2jc5: Apurinic Apyrimidinic (AP) endonuclease (NApe) from Neisseria Men... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jc5 | ||||||
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Title | Apurinic Apyrimidinic (AP) endonuclease (NApe) from Neisseria Meningitidis | ||||||
Components | EXODEOXYRIBONUCLEASE | ||||||
Keywords | HYDROLASE / NEISSERIA MENINGITIDIS / REPAIR PHOSPHODIESTERASE / DNA REPAIR / EXONUCLEASE / ENDONUCLEASE | ||||||
Function / homology | Function and homology information exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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.S. / 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 | 2jc5.cif.gz | 229.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jc5.ent.gz | 185.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jc5 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jc5 | HTTPS FTP |
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-Related structure data
Related structure data | 2jc4C 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: 29699.594 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: Q7DD47, exodeoxyribonuclease III |
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-Non-polymers , 5 types, 319 molecules
#2: Chemical | ChemComp-MG / | ||||
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#3: Chemical | ChemComp-BCN / | ||||
#4: Chemical | #5: Chemical | #6: 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: 2.01 Å3/Da / Density % sol: 38.5 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 9 Details: 24 WELL LINBRO PLATES USED FOR HANGING DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH 7.0 AND 100 MM NACL. THE ...Details: 24 WELL LINBRO PLATES USED FOR HANGING DROP EXPERIMENTS WITH 0.5 UL PROTEIN AND 0.5 UL WELL SOLUTION FOR THE DROPS. PROTEIN CONCENTRATION 20 MG/ML, IN 10 MM TRIS, PH 7.0 AND 100 MM NACL. THE WELL SOLUTION CONTAINED 20% PEG 20000, 0.1 M BICINE PH 9.0, 2% DIOXANE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 21, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 35560 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 9.64 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.5 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BIX Resolution: 1.5→29.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.298 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE ATOMS MISSING FROM THE SIDECHAINS BECAUSE THERE WAS NO DENSITY FOR THESE ATOMS IN THE ELECTRON DENSITY MAPS ARG ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES HAVE ATOMS MISSING FROM THE SIDECHAINS BECAUSE THERE WAS NO DENSITY FOR THESE ATOMS IN THE ELECTRON DENSITY MAPS ARG 64, ARG 75, GLU 87, GLU 177, LYS 181, LYS 185, AND GLU 259.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.53 Å
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Refine LS restraints |
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