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- PDB-2x2j: Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x2j | ||||||
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Title | Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-glucan lyase with deoxynojirimycin | ||||||
![]() | ALPHA-1,4-GLUCAN LYASE ISOZYME 1 | ||||||
![]() | LYASE / STARCH BINDING DOMAIN / ANHYDROFRUCTOSE PATHWAY / GLYCOSIDE HYDROLASE FAMILY 31 | ||||||
Function / homology | ![]() exo-(1,4)-alpha-D-glucan lyase activity / glucosidase II complex / alpha-glucosidase activity / N-glycan processing / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: Crystal Structure of Alpha-1,4-Glucan Lyase, a Unique Glycoside Hydrolase Family Member with a Novel Catalytic Mechanism. Authors: Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Zhang, R. / Dijkstra, B.W. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 510.5 KB | Display | ![]() |
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Full document | ![]() | 571.1 KB | Display | |
Data in XML | ![]() | 153.8 KB | Display | |
Data in CIF | ![]() | 217.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x2hSC ![]() 2x2iC ![]() 4amwC ![]() 4amxC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: NOJ / End label comp-ID: NOJ / Refine code: 4 / Auth seq-ID: 14 - 1050 / Label seq-ID: 3
NCS oper:
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Components
#1: Protein | Mass: 116062.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 62-1088 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: REPLICATING VECTOR WITH HARS SEQUENCE. COLLECTED AT TAPING BAY, TSINGTAO, CHINA Production host: ![]() #2: Chemical | ChemComp-NOJ / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Sequence details | FIRST 50 AMINO ACIDS ARE A SIGNAL PEPTIDE. THE NEXT 11 AMINO ACIDS ARE NOT PRESENT IN THE ENZYME. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18-21% PEG 8000, 0.1 M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 1, 2007 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 175340 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1 / % possible all: 85.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2X2H Resolution: 2.35→33.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 27.018 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.625 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. U VALUES WITH TLS ADDED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→33.19 Å
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Refine LS restraints |
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