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- PDB-2vnc: Crystal structure of Glycogen Debranching enzyme TreX from Sulfol... -

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Basic information

Entry
Database: PDB / ID: 2vnc
TitleCrystal structure of Glycogen Debranching enzyme TreX from Sulfolobus solfataricus
ComponentsGLYCOGEN OPERON PROTEIN GLGX
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


: / glycogen catabolic process / aminopeptidase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycogen debranching enzyme, GlgX type / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Glycogen debranching enzyme, GlgX type / Glycogen debranching enzyme GlgX/isoamylase, N-terminal Early set domain / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Alpha amylase, C-terminal all-beta domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glycogen debranching enzyme
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSong, H.-N. / Yoon, S.-M. / Cha, H. / Park, K.-T. / Woo, E.-J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Insight Into the Bifunctional Mechanism of the Glycogen-Debranching Enzyme Trex from the Archaeon Sulfolobus Solfataricus.
Authors: Woo, E.-J. / Lee, S. / Cha, H. / Park, J.-T. / Yoon, S.-M. / Song, H.-M. / Park, K.-H.
History
DepositionFeb 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX


Theoretical massNumber of molelcules
Total (without water)166,3642
Polymers166,3642
Non-polymers00
Water2,342130
1
A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX

A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX


Theoretical massNumber of molelcules
Total (without water)332,7274
Polymers332,7274
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-15.2 kcal/mol
Surface area51180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.077, 136.077, 173.545
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein GLYCOGEN OPERON PROTEIN GLGX / GLYCOGEN DEBRANCHING ENZYME / TREX


Mass: 83181.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DISULFIDE BOND BETWEEN A 254 AND A 261 / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P95868, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 57.78 % / Description: NONE
Crystal growpH: 8.5 / Details: 2.2M AMMONIUM PHOSPHATE, 0.1M TRIS-HCL (PH 8.5)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2399
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 51429 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.75 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BF2

1bf2


Resolution: 3→29.91 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.85 / SU B: 44.982 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1909 5.1 %RANDOM
Rwork0.215 ---
obs0.218 35743 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 3→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11154 0 0 130 11284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211473
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.94815562
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26851360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69724.29606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.584151913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7681573
X-RAY DIFFRACTIONr_chiral_restr0.1010.21626
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028956
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.26077
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.27707
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7341.56945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.325211002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.53435196
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4394.54560
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 134
Rwork0.225 2584

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