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- PDB-2vr5: Crystal structure of Trex from Sulfolobus Solfataricus in complex... -

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Basic information

Entry
Database: PDB / ID: 2vr5
TitleCrystal structure of Trex from Sulfolobus Solfataricus in complex with acarbose intermediate and glucose
ComponentsGLYCOGEN OPERON PROTEIN GLGX
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


glycogen debranching enzyme activity / glycogen catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / aminopeptidase activity
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 / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-A16 / alpha-D-glucopyranose / Glycogen debranching enzyme
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsSong, H.-N. / Yoon, S.-M. / Lee, S.-J. / Cha, H.-J. / Park, K.-H. / 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. / Lee, S. / Cha, H. / Park, J. / Yoon, S. / Song, H. / Park, K.
History
DepositionMar 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)168,24310
Polymers166,3642
Non-polymers1,8808
Water7,224401
1
A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX
hetero molecules

A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX
hetero molecules

A: GLYCOGEN OPERON PROTEIN GLGX
B: GLYCOGEN OPERON PROTEIN GLGX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,73030
Polymers499,0916
Non-polymers5,63924
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area26690 Å2
ΔGint-90.2 kcal/mol
Surface area141220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.814, 204.814, 89.558
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein / Sugars , 2 types, 6 molecules AB

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


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, A 505 AND A 519, B 254 AND B 261, B 505 AND B 519
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: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 405 molecules

#3: Chemical ChemComp-A16 / 4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose


Mass: 485.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H35NO13
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.33 % / Description: NONE
Crystal growpH: 8
Details: PEG 3K 8%, 0.2M LITHIUM SULFATE, 0.1M PH 8.0 IMIDAZOLE BUFFER

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 51526 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 3.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.7 / % possible all: 93

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2VNC

2vnc


Resolution: 2.8→29.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 48122.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2573 5 %RANDOM
Rwork0.214 ---
obs0.214 51460 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.557 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.08 Å20 Å20 Å2
2--9.08 Å20 Å2
3----18.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11685 0 123 401 12209
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.341.5
X-RAY DIFFRACTIONc_mcangle_it6.342
X-RAY DIFFRACTIONc_scbond_it6.612
X-RAY DIFFRACTIONc_scangle_it8.452.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 403 4.9 %
Rwork0.329 7824 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADR2_PAR.TXTADR2_TOP.TXT
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4GLC_PAR.TXTGLC_TOP.TXT
X-RAY DIFFRACTION5GOL_PAR.TXTGOL_TOP.TXT

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