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- PDB-2gdv: Sucrose phosphorylase from BIFIDOBACTERIUM ADOLESCENTIS reacted w... -

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Basic information

Entry
Database: PDB / ID: 2gdv
TitleSucrose phosphorylase from BIFIDOBACTERIUM ADOLESCENTIS reacted with sucrose
Componentssucrose phosphorylase
KeywordsTRANSFERASE / BETA-ALPHA-BARRELS / DIMER / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


sucrose phosphorylase / sucrose phosphorylase activity / carbohydrate metabolic process
Similarity search - Function
alpha-Amylases / Sucrose phosphorylase, C-terminal / Sucrose phosphorylase, C-terminal / Glycosyl hydrolase fold / Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain ...alpha-Amylases / Sucrose phosphorylase, C-terminal / Sucrose phosphorylase, C-terminal / Glycosyl hydrolase fold / Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Single Sheet / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Sucrose phosphorylase / Sucrose phosphorylase
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSkov, L.K. / Mirza, O. / Gajhede, M. / Katsrup, J.S.
CitationJournal: To be Published
Title: Structural rearrangements of Sucrose Phosphorylase from Bifidobacterium adolescentis during sucrose conversion
Authors: Mirza, O. / Skov, L.K. / Sprogoe, D. / Van den Broek, L.A.M. / Voragen, A.G.J. / Katsrup, J.S. / Gajhede, M.
History
DepositionMar 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sucrose phosphorylase
B: sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8664
Polymers112,5052
Non-polymers3602
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.740, 103.070, 150.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein sucrose phosphorylase /


Mass: 56252.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (bacteria)
Plasmid: PBLUESCRIPT / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 BLUE MRF
References: UniProt: Q84HQ2, UniProt: A0ZZH6*PLUS, sucrose phosphorylase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, SODIUM ACETATE, TRIS, bicine, sucrose, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.841 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.841 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 80388 / Num. obs: 80388 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.5
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.6 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.701data extraction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R7A

1r7a


Resolution: 2→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2665797.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4028 5 %RANDOM
Rwork0.198 ---
obs0.2 79924 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.738 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.94 Å20 Å20 Å2
2--8.28 Å20 Å2
3----4.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7930 0 23 1006 8959
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 619 4.8 %
Rwork0.273 12314 -
obs-12933 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein10.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION4int2.paramint2.top

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