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Yorodumi- PDB-2nm3: Crystal structure of dihydroneopterin aldolase from S. aureus in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nm3 | ||||||
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Title | Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2S)-monapterin at 1.68 angstrom resolution | ||||||
Components | Dihydroneopterin aldolase | ||||||
Keywords | LYASE / Dihydroneopterin aldolase / dhna / substrate complex / monapterin / neopterin / 7 / 8-dihydromonapterin / drug design | ||||||
Function / homology | Function and homology information 7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / isomerase activity / tetrahydrofolate biosynthetic process Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Blaszczyk, J. / Ji, X. / Yan, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural basis for the aldolase and epimerase activities of Staphylococcus aureus dihydroneopterin aldolase. Authors: Blaszczyk, J. / Li, Y. / Gan, J. / Yan, H. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nm3.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nm3.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/2nm3 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/2nm3 | HTTPS FTP |
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-Related structure data
Related structure data | 2nm2C 1dhnS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 13769.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folB / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / Strain (production host): PLYSS / References: UniProt: P56740, dihydroneopterin aldolase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-MPU / |
#4: 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: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 292 K / pH: 6.5 Details: 1.4M Sodium acetate, 0.2M Imidazole, 0.1M Sodium cacodylate, 10mM Tris-HCL, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2004 / Details: MIRROR |
Radiation | Monochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30 Å / Num. obs: 13718 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 10.472 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.32 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 9.31 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.09 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DHN Resolution: 1.68→30 Å / Num. parameters: 3441 / Num. restraintsaints: 4065 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER Details: LEAST-SQUARES REFINEMENT USING THE KONNERT-HENDRICKSON CONJUGATE-GRADIENT ALGORITHM
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91 (1975) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1156.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.77 Å /
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