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Yorodumi- PDB-2hln: L-asparaginase from Erwinia carotovora in complex with glutamic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hln | ||||||
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Title | L-asparaginase from Erwinia carotovora in complex with glutamic acid | ||||||
Components | L-asparaginase | ||||||
Keywords | HYDROLASE / L-asparaginase / Erwinia carotovora | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pectobacterium atrosepticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Kravchenko, O.V. / Kislitsin, Y.A. / Popov, A.N. / Nikonov, S.V. / Kuranova, I.P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Three-dimensional structures of L-asparaginase from Erwinia carotovora complexed with aspartate and glutamate. Authors: Kravchenko, O.V. / Kislitsin, Y.A. / Popov, A.N. / Nikonov, S.V. / Kuranova, I.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hln.cif.gz | 721 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hln.ent.gz | 595.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hln_validation.pdf.gz | 555.1 KB | Display | wwPDB validaton report |
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Full document | 2hln_full_validation.pdf.gz | 592.9 KB | Display | |
Data in XML | 2hln_validation.xml.gz | 146.8 KB | Display | |
Data in CIF | 2hln_validation.cif.gz | 200.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/2hln ftp://data.pdbj.org/pub/pdb/validation_reports/hl/2hln | HTTPS FTP |
-Related structure data
Related structure data | 2gvnC 1zcfS 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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2 |
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3 |
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Unit cell |
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Details | The biological unit is tetramer. There are 3 biological units in the asymmetric unit. The biological unit 1 consists of chains A,B,E,F. The biological unit 2 consists of chains C,D,G,H. The biological unit 3 consists of chains I,J,K,L. |
-Components
#1: Protein | Mass: 34528.266 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Gene: lanS / Plasmid: pACYCLANS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7WWK9, asparaginase #2: Chemical | ChemComp-GLU / #3: Chemical | ChemComp-PEG / #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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1% sodium cacodilate, 8% PEG MME 5000, 0.06% octylglucoside, 0.08M glutamic acid, 0.02% sodium azide, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.99 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2005 / Details: bent mirror |
Radiation | Monochromator: double crystal focussing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 180862 / Num. obs: 180862 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.2→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5910 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ZCF Resolution: 2.2→19.98 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.208 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.385 / ESU R Free: 0.258 / 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: 43.142 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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