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Yorodumi- PDB-1rs4: DHNA, 7,8-Dihydroneopterin Aldolase complexed with 3-(5-Amino-7-h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rs4 | ||||||
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Title | DHNA, 7,8-Dihydroneopterin Aldolase complexed with 3-(5-Amino-7-hydroxy-[1,2,3]triazolo[4,5-d]pyrimidin-2-yl)-N-(3,5-dichlorobenzyl)-benzamide | ||||||
Components | Dihydroneopterin aldolase | ||||||
Keywords | LYASE / DHNA / 7 / 8-Dihydroneopterin-(5-Amino-7-hydroxy-[1 / 2 / 3]triazolo[4 / 5-d]pyrimidin-2-yl)-N-(3 / 5-dichlorobenzyl)-benzamide Aldolase | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.7 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 | 1rs4.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rs4.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rs4_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 1rs4_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 1rs4_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1rs4_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/1rs4 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/1rs4 | HTTPS FTP |
-Related structure data
Related structure data | 1rriC 1rrwC 1rryC 1rs2C 1rsdC 1rsiC 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-45P / |
-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 | Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP |
-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: 2.7→19.27 Å / Num. obs: 2989 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35.9 Å2 |
Reflection shell | Resolution: 2.7→2.87 Å / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→19.27 Å / Rfactor Rfree error: 0.024 / Data cutoff high absF: 209548.5 / 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: 23.4453 Å2 / ksol: 0.275019 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.093 / Total num. of bins used: 6
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Xplor file |
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