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Open data
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Basic information
Entry | Database: PDB / ID: 1kqy | |||||||||
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Title | Hevamine Mutant D125A/E127A/Y183F in Complex with Penta-NAG | |||||||||
![]() | Hevamine A | |||||||||
![]() | HYDROLASE / chitinase/lysozyme | |||||||||
Function / homology | ![]() chitinase / vacuole / chitinase activity / chitin catabolic process / polysaccharide catabolic process / lysozyme / lysozyme activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rozeboom, H.J. / Dijkstra, B.W. | |||||||||
![]() | ![]() Title: Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis. Authors: Bokma, E. / Rozeboom, H.J. / Sibbald, M. / Dijkstra, B.W. / Beintema, J.J. #1: ![]() Title: The 1.8 A Resolution Structure of Hevamine, a Plant Chitinase/Lysozyme, and Analysis of the Conserved Sequence and Structure Motifs of Glycosyl Hydrolase Family 18. Authors: Terwisscha van Scheltinga, A.C. / Hennig, M. / Dijkstra, B.W. #2: ![]() Title: Stereochemistry of Chitin Hydrolysis by a Plant Chitinase/Lysozyme and X-ray Structure of a Complex with Allosamidin: Evidence for Substrate Assisted Catalysis. Authors: Terwisscha van Scheltinga, A.C. / Armand, S. / Kalk, K.H. / Isogai, A. / Henrissat, B. / Dijkstra, B.W. #3: ![]() Title: Crystal Structures of Hevamine, a Plant Defence Protein with Chitinase and Lysozyme Activity, and its Complex with an Inhibitor. Authors: Terwisscha van Scheltinga, A.C. / Kalk, K.H. / Beintema, J.J. / Dijkstra, B.W. #4: ![]() Title: Crystallization of Hevamine, an Enzyme with Lysozyme/Chitinase Activity from Hevea brasiliensis Latex. Authors: Rozeboom, H.J. / Budiani, A. / Beintema, J.J. / Dijkstra, B.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.6 KB | Display | ![]() |
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PDB format | ![]() | 54.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kqzC ![]() 1kr0C ![]() 1kr1C ![]() 2hvmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29455.139 Da / Num. of mol.: 1 / Mutation: D125A/E127A/Y183F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: p23472, UniProt: P23472*PLUS, chitinase, lysozyme | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 1.1-1.4 M / Common name: ammonium sulfate / Details: or 10-30%(w/v) PEG3350, pH7.0 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 31, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. all: 18817 / Num. obs: 18817 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.92→1.95 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.7 / Num. unique all: 918 / % possible all: 99.2 |
Reflection | *PLUS Lowest resolution: 43.5 Å / Num. obs: 18861 / Num. measured all: 118829 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 99.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HVM Resolution: 1.92→43.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1327255.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.4526 Å2 / ksol: 0.373973 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.92→43.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.99 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.167 / Rfactor Rfree: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.268 / % reflection Rfree: 5.5 % / Rfactor Rwork: 0.216 |