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Yorodumi- PDB-3ic1: Crystal structure of zinc-bound succinyl-diaminopimelate desuccin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ic1 | ||||||
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Title | Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae | ||||||
Components | Succinyl-diaminopimelate desuccinylase | ||||||
Keywords | HYDROLASE / DapE / PSI2 / MCSG / Zn bound / succinyl-diaminopimelate desuccinylase / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Amino-acid biosynthesis / Cobalt / Diaminopimelate biosynthesis / Lysine biosynthesis / Metal-binding | ||||||
Function / homology | Function and homology information succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nocek, B.P. / Gillner, D.M. / Holz, R.C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase. Authors: Nocek, B.P. / Gillner, D.M. / Fan, Y. / Holz, R.C. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ic1.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ic1.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ic1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ic1_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 3ic1_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 3ic1_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 3ic1_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/3ic1 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/3ic1 | HTTPS FTP |
-Related structure data
Related structure data | 3iszC 1vgyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41397.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: dapE, HI0102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: P44514, succinyl-diaminopimelate desuccinylase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2 M NaCl, 0.1 M NaAcetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2009 / Details: double crystal |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 36163 / Num. obs: 34773 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VGY Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.83 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.366 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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