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Yorodumi- PDB-1gxs: Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxs | |||||||||
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Title | Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with Inhibitor Benzoic Acid: a novel cyanogenic enzyme | |||||||||
Components | (P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN ...) x 2 | |||||||||
Keywords | LYASE / INHIBITOR COMPLEX / CYANOGENESIS MECHANISM | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | SORGHUM BICOLOR (sorghum) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Lauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal Structure of Hydroxynitrile Lyase from Sorghum Bicolor in Complex with the Inhibitor Benzoic Acid: A Novel Cyanogenic Enzyme Authors: Lauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gxs.cif.gz | 190.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gxs.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gxs_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1gxs_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1gxs_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 1gxs_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxs ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxs | HTTPS FTP |
-Related structure data
Related structure data | 3sc2S 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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Details | THE BIOLOGICALLY ACTIVE SUBUNIT IS A HETEROTETRAMER FORMED BY TWO AB-HETERODIMERS |
-Components
-P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 30395.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOENZYME II / Source: (natural) SORGHUM BICOLOR (sorghum) / Tissue: PRIMARY LEAVES OF SEEDLINGS References: UniProt: Q8W4X3, UniProt: P52708*PLUS, hydroxymandelonitrile lyase #2: Protein | Mass: 17713.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOENZYME II / Source: (natural) SORGHUM BICOLOR (sorghum) / Tissue: PRIMARY LEAVES OF SEEDLINGS References: UniProt: Q8W4X3, UniProt: P52708*PLUS, hydroxymandelonitrile lyase |
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-Sugars , 2 types, 4 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 3 types, 335 molecules
#4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | VARIANTS LISTED IN SEQADV RECORDS WERE SUPPLIED BY THE AUTHORS OF THE PDB ENTRY, AND WERE NOT ...VARIANTS LISTED IN SEQADV RECORDS WERE SUPPLIED BY THE AUTHORS OF THE PDB ENTRY, AND WERE NOT OBTAINED FROM THE SWISS-PROT ENTRY |
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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: 3.16 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 Details: 100MM NA-CITRATE PH 5.4 USING 1.6 M AMMONIUM SULFATE | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Lauble, H., (1996) Acta Crystallogr., D52, 887. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 291 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→17 Å / Num. obs: 100992 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 15.6 Å2 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.7 / % possible all: 82.9 |
Reflection | *PLUS Lowest resolution: 17 Å / Num. obs: 51747 / Num. measured all: 100992 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 82.9 % / Rmerge(I) obs: 0.114 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SC2 Resolution: 2.3→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: ASYMMETRIC UNIT CONTAINS 2 ALPHA/ BETA-DIMERS
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Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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