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- PDB-7jnd: The structure of CBM32-1 and CBM32-2 domains from Clostridium per... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jnd | |||||||||
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Title | The structure of CBM32-1 and CBM32-2 domains from Clostridium perfringens ZmpB | |||||||||
![]() | F5/8 type C domain protein | |||||||||
![]() | SUGAR BINDING PROTEIN / Carbohydrate binding module | |||||||||
Function / homology | ![]() hydrolase activity, acting on glycosyl bonds / metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Pluvinage, B. / Boraston, A.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecturally complex O -glycopeptidases are customized for mucin recognition and hydrolysis. Authors: Pluvinage, B. / Ficko-Blean, E. / Noach, I. / Stuart, C. / Thompson, N. / McClure, H. / Buenbrazo, N. / Wakarchuk, W. / Boraston, A.B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.1 KB | Display | ![]() |
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PDB format | ![]() | 71.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.6 KB | Display | ![]() |
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Full document | ![]() | 438.1 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jfsC ![]() 7jnbSC ![]() 7jnfC ![]() 7jrlC ![]() 7jrmC ![]() 7js4C 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: 51421.480 Da / Num. of mol.: 1 / Fragment: Carbohydrate binding module (UNP residues 28-453) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A Gene: CPF_1489 / Plasmid: pET28a / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.18 M calcium chloride, 20% PEG3350, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91966 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.53 Å / Num. obs: 31552 / % possible obs: 96.5 % / Redundancy: 6.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.069 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4198 / CC1/2: 0.756 / Rpim(I) all: 0.285 / % possible all: 89.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 7JNB Resolution: 2→41.16 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.039 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.65 Å2 / Biso mean: 30.224 Å2 / Biso min: 13.9 Å2
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Refinement step | Cycle: final / Resolution: 2→41.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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