+Open data
-Basic information
Entry | Database: PDB / ID: 1rsi | ||||||
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Title | DHNA complex with 2-Amino-5-bromo-3-hydroxy-6-phenylpyrimidine | ||||||
Components | Dihydroneopterin aldolase | ||||||
Keywords | LYASE / DHNA / 7 / 8-Dihydroneopterin Aldolase / 2-Amino-5-bromo-3-hydroxy-6-phenylpyrimidine | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. ...Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / Severin, J.M. / Walter, K.A. / Magdalinos, P. / Jakob, C.G. / Wagner, R. / Beutel, B.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization. Authors: Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / ...Authors: Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / Severin, J.M. / Walter, K.A. / Magdalinos, P. / Jakob, C.G. / Wagner, R. / Beutel, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rsi.cif.gz | 35.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rsi.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/1rsi ftp://data.pdbj.org/pub/pdb/validation_reports/rs/1rsi | HTTPS FTP |
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-Related structure data
Related structure data | 1rriC 1rrwC 1rryC 1rs2C 1rs4C 1rsdC 1u68C C: citing same article (ref.) |
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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
#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P56740, dihydroneopterin aldolase |
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#2: Chemical | ChemComp-977 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M Ammonium Acetate, 0.1 M tri-sodium citrate, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34.15 Å / Num. all: 25032 / Num. obs: 5864 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.6 Å2 |
Reflection shell | Resolution: 2.2→2.34 Å / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→34.15 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 200038.35 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.107486 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→34.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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