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Yorodumi- PDB-4r41: Complex Crystal structure of 4-nitro-2-phosphono-benzoic acid wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r41 | ||||||
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Title | Complex Crystal structure of 4-nitro-2-phosphono-benzoic acid with sp-Aspartate-Semialdehyde Dehydrogenase and Nicotinamide-dinucleotide | ||||||
Components | Aspartate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADP binding | ||||||
Function / homology | Function and homology information Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.61 Å | ||||||
Authors | Pavlovsky, A.G. / Viola, R.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway. Authors: Pavlovsky, A.G. / Thangavelu, B. / Bhansali, P. / Viola, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r41.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r41.ent.gz | 123.3 KB | Display | PDB format |
PDBx/mmJSON format | 4r41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r41_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4r41_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4r41_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 4r41_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/4r41 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/4r41 | HTTPS FTP |
-Related structure data
Related structure data | 4r3nSC 4r3wC 4r4jC 4r51C 4r54C 4r5hC 4r5mC S: Starting model for refinement 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40038.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP23-BS72 / Gene: asd, CGSSp23BS72_03388 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A5MTN0, aspartate-semialdehyde dehydrogenase |
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-Non-polymers , 6 types, 344 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: 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: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15-22% PEG 3350, 0.1 M Na-acetate, 0.1 M MES buffer (pH 6.5), 10mM TCEP, 3% Ethylene Glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 27, 2012 Details: double crystal monochromator and K-B pair of biomorph mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 92850 / Num. obs: 82360 / % possible obs: 88.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 9.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 4R3N Resolution: 1.61→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.411 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.105 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.977 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.61→50 Å
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Refine LS restraints |
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