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Yorodumi- PDB-2dhn: COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AURE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dhn | ||||||
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Title | COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 2.2 A RESOLUTION | ||||||
Components | 7,8-DIHYDRONEOPTERIN ALDOLASE | ||||||
Keywords | PRODUCT COMPLEX / PTERINE BINDING / FOLATE BIOSYNTHESIS / ANTIBIOTIC TARGET / BETA-BARREL | ||||||
Function / homology | Function and homology information 7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / isomerase activity Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Hennig, M. / D'Arcy, A. / Hampele, I.C. / Page, M.G.P. / Oefner, C.H. / Dale, G. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from Staphylococcus aureus. Authors: Hennig, M. / D'Arcy, A. / Hampele, I.C. / Page, M.G. / Oefner, C. / Dale, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dhn.cif.gz | 37.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dhn.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dhn_validation.pdf.gz | 385.6 KB | Display | wwPDB validaton report |
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Full document | 2dhn_full_validation.pdf.gz | 387.6 KB | Display | |
Data in XML | 2dhn_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 2dhn_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/2dhn ftp://data.pdbj.org/pub/pdb/validation_reports/dh/2dhn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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: DHNA / Plasmid: PSADHNA / Production host: Escherichia coli (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: P56740 |
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#2: Chemical | ChemComp-PH2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow | pH: 6.6 / Details: pH 6.6 | |||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1997 / Details: MIRROR |
Radiation | Monochromator: SUPPER MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 27653 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.9 / % possible all: 98.6 |
Reflection | *PLUS Num. obs: 6008 / Num. measured all: 27653 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: DHNA UNLIGANDED Resolution: 2.2→30 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: RFREE / σ(F): 0
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Displacement parameters | Biso mean: 24.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |