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- PDB-2jkp: Structure of a family 97 alpha-glucosidase from Bacteroides theta... -

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Basic information

Entry
Database: PDB / ID: 2jkp
TitleStructure of a family 97 alpha-glucosidase from Bacteroides thetaiotaomicron in complex with castanospermine
ComponentsALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB)
KeywordsHYDROLASE / FAMILY 97 / CASTANOSPERMINE / ALPHA-GLUCOSIDASE / GLYCOSIDE HYDROLASE / BACTEROIDES THETAIOTAOMICRON
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / starch catabolic process / carbohydrate binding / periplasmic space / calcium ion binding / plasma membrane
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich ...Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CASTANOSPERMINE / Glucan 1,4-alpha-glucosidase SusB / Glucan 1,4-alpha-glucosidase SusB
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsGloster, T.M. / Turkenburg, J.P. / Potts, J.R. / Henrissat, B. / Davies, G.J.
CitationJournal: Chem.Biol. / Year: 2008
Title: Divergence of Catalytic Mechanism within a Glycosidase Family Provides Insight Into Evolution of Carbohydrate Metabolism by Human Gut Flora.
Authors: Gloster, T.M. / Turkenburg, J.P. / Potts, J.R. / Henrissat, B. / Davies, G.J.
History
DepositionAug 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB)
B: ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,32110
Polymers166,6152
Non-polymers7078
Water22,6091255
1
A: ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6615
Polymers83,3071
Non-polymers3534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6615
Polymers83,3071
Non-polymers3534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.566, 111.988, 104.134
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB) / ALPHA-GLUCOSIDASE


Mass: 83307.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P71094, UniProt: G8JZS4*PLUS, alpha-glucosidase
#2: Chemical ChemComp-CTS / CASTANOSPERMINE / (1S,6S,7R,8R,8AR)-1,6,7,8-TETRAHYDROXYINDOLIZIDINE / Castanospermine


Mass: 189.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO4 / Comment: antivirus, inhibitor, alkaloid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1255 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 21 RESIDUES OF THE GENE CORRESPOND TO A SIGNAL PEPTIDE SEQUENCE AND WERE NOT CLONED INTO ...THE FIRST 21 RESIDUES OF THE GENE CORRESPOND TO A SIGNAL PEPTIDE SEQUENCE AND WERE NOT CLONED INTO THE VECTOR. NUMBERING IN THE PDB CORRESPONDS TO THE FULL LENGTH GENE ( IE. STARTS AT GLN22). THE FIRST 10 RESIDUES OF THE SEQUENCE CRYSTALLISED CORRESPOND TO A HIS TAG INTRODUCED DURING THE CLONING PROCEDURE.

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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: 2.9 Å3/Da / Density % sol: 58 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growDetails: 18-22% POLYETHYLENE GLYCOL 3350 AND 0.02 M SODIUM/POTASSIUM PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 108971 / % possible obs: 95.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 69.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JKA

2jka


Resolution: 1.99→102.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.329 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 5452 5 %RANDOM
Rwork0.173 ---
obs0.176 103399 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-2.26 Å2
2--0.29 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.99→102.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11024 0 44 1255 12323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211543
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.93615714
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68251429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17524.671578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.426151912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2791550
X-RAY DIFFRACTIONr_chiral_restr0.1050.21663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218968
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7531.56922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29211213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17634621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2144.54471
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: 1.99→2.04 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 252
Rwork0.262 4981

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