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Yorodumi- PDB-12as: ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 12as | ||||||
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Title | ASPARAGINE SYNTHETASE MUTANT C51A, C315A COMPLEXED WITH L-ASPARAGINE AND AMP | ||||||
Components | ASPARAGINE SYNTHETASE | ||||||
Keywords | LIGASE / ASPARAGINE SYNTHETASE / NITROGEN FIXATION | ||||||
Function / homology | Function and homology information aspartate-ammonia ligase / aspartate-ammonia ligase activity / L-asparagine biosynthetic process / asparagine biosynthetic process / DNA damage response / protein homodimerization activity / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Nakatsu, T. / Kato, H. / Oda, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase. Authors: Nakatsu, T. / Kato, H. / Oda, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary Crystallographic Study of Asparagine Synthetase from Escherichia Coli Authors: Nakatsu, T. / Kato, H. / Oda, J. #2: Journal: Biosci.Biotechnol.Biochem. / Year: 1992 Title: Overexpression and Purification of Asparagine Synthetase from Escherichia Coli Authors: Sugiyama, A. / Kato, H. / Nishioka, T. / Oda, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 12as.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb12as.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 12as.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 12as_validation.pdf.gz | 505.9 KB | Display | wwPDB validaton report |
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Full document | 12as_full_validation.pdf.gz | 527.4 KB | Display | |
Data in XML | 12as_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 12as_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/2a/12as ftp://data.pdbj.org/pub/pdb/validation_reports/2a/12as | HTTPS FTP |
-Related structure data
Related structure data | 11asSC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.00022, 0.00086), Vector: |
-Components
#1: Protein | Mass: 36633.367 Da / Num. of mol.: 2 / Mutation: C51A, C315A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ASNA / Plasmid: PUNAD37 CYS-FREE / Gene (production host): ASNA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00963, aspartate-ammonia ligase #2: Chemical | #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN CRYSTALLIZED FROM 45% SATURATED AMMONIUM SULFATE, 22 MM ASPARAGINE, 88 MM MGCL2, 10 %(W/V) GLYCEROL 5 MM 2-MERCAPTOETHANOL, 50 MM HEPES, PH7.5 THEN SOAKED BY 50MM AMP AND 50 MM ASPARAGINE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRROR |
Radiation | Monochromator: MSC DOUBLE MIRROR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. obs: 25168 / % possible obs: 72.1 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.2 / % possible all: 53.4 |
Reflection | *PLUS Num. measured all: 71426 |
Reflection shell | *PLUS % possible obs: 53.4 % |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 11AS Resolution: 2.2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 10.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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