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Yorodumi- PDB-1cqd: THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cqd | |||||||||
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Title | THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE | |||||||||
Components | PROTEIN (PROTEASE II) | |||||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE / GLYCOPROTEIN / PROLINE SPECIFICITY / CARBOHYDRATE / PAPAIN FAMILY | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Zingiber officinale (ginger) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Choi, K.H. / Laursen, R.A. / Allen, K.N. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 Title: The 2.1 A structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale. Authors: Choi, K.H. / Laursen, R.A. / Allen, K.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cqd.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cqd.ent.gz | 148.2 KB | Display | PDB format |
PDBx/mmJSON format | 1cqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cqd_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 1cqd_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1cqd_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 1cqd_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cqd ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cqd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23941.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED FROM GROUND GINGER ROOT / Source: (natural) Zingiber officinale (ginger) / References: UniProt: P82474 |
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-Sugars , 4 types, 6 molecules
#2: Polysaccharide | beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 377 molecules
#5: Chemical | ChemComp-THJ / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THIOSULFATSequence details | THE SEQUENCE IS TO BE PUBLISHED IN A SEQUENCE DATABASE. | |
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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: 2.19 Å3/Da / Density % sol: 43.38 % Description: INITIAL MODEL WAS GENERATED FROM PAPAIN, ACTINIDIN AND PROTEASE OMEGA BY SWISS- MODEL PROTEIN MODELING SERVER | |||||||||||||||||||||||||
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Crystal grow | pH: 5.2 Details: 0.1 M SODIUM ACETATE BUFFER (PH 5.2) CONTAINING 0.1 M AMMONIUM SULFATE, 26% POLYETHYLENE GLYCOL MONOMETHYLETHER 2000, AND 2.5 MM SODIUM TETRATHIONATE | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: SUPPER LONG MIRRORS |
Radiation | Monochromator: SUPPER LONG MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 58449 / % possible obs: 99.7 % / Redundancy: 5 % / Rsym value: 0.191 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / % possible all: 75 |
Reflection | *PLUS Rmerge(I) obs: 0.191 |
Reflection shell | *PLUS % possible obs: 94.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 13.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.214 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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