+Open data
-Basic information
Entry | Database: PDB / ID: 4pvp | |||||||||
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Title | Crystal structure of malonate-bound human L-asparaginase protein | |||||||||
Components | Isoaspartyl peptidase/L-asparaginase | |||||||||
Keywords | HYDROLASE / NTN ENZYME / HOMODIMER / L-ASPARAGINE | |||||||||
Function / homology | Function and homology information asparagine catabolic process via L-aspartate / beta-aspartyl-peptidase / Phenylalanine metabolism / asparaginase / asparaginase activity / beta-aspartyl-peptidase activity / photoreceptor inner segment / proteolysis / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Nomme, J. / Lavie, A. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structures of apo and product-bound human L-asparaginase: insights into the mechanism of autoproteolysis and substrate hydrolysis. Authors: Nomme, J. / Su, Y. / Konrad, M. / Lavie, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pvp.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pvp.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pvp_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 4pvp_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 4pvp_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 4pvp_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/4pvp ftp://data.pdbj.org/pub/pdb/validation_reports/pv/4pvp | HTTPS FTP |
-Related structure data
Related structure data | 4pvqC 4pvrC 4pvsC 2zakS C: citing same article (ref.) S: Starting model for refinement |
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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: 32289.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALP, ASRGL1, CRASH / Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) C41 References: UniProt: Q7L266, beta-aspartyl-peptidase, asparaginase #2: Chemical | ChemComp-MLI / | #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: 2.27 Å3/Da / Density % sol: 45.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.2M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 11, 2011 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.85→30 Å / Num. all: 48285 / Num. obs: 48285 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.047 / Net I/σ(I): 18.4 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.96 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.58 / Rsym value: 0.249 / % possible all: 69.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2ZAK Resolution: 1.85→29.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.509 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.89 Å / Total num. of bins used: 20
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