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- PDB-6fme: Structure of sucrose phosphorylase from Bifidobacterium adolescen... -

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Basic information

Entry
Database: PDB / ID: 6fme
TitleStructure of sucrose phosphorylase from Bifidobacterium adolescentis bound to glycosylated resveratrol
ComponentsSucrose phosphorylase
KeywordsTRANSFERASE / sucrose phosphorylase / resveratrol / enzyme design
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
Sucrose phosphorylase
Similarity search - Component
Biological speciesBifidobacterium adolescentis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsGrimm, C. / Kraus, M.
CitationJournal: To Be Published
Title: Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to glycosylated resveratrol
Authors: Grimm, C.
History
DepositionJan 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,1966
Polymers112,8282
Non-polymers3684
Water20,8251156
1
B: Sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5983
Polymers56,4141
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5983
Polymers56,4141
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.010, 101.925, 152.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sucrose phosphorylase / SPase


Mass: 56413.867 Da / Num. of mol.: 2 / Mutation: Q345F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a) (bacteria)
Strain: ATCC 15703 / DSM 20083 / NCTC 11814 / E194a / Gene: sucP, spl, BAD_0078 / Production host: Escherichia coli (E. coli) / References: UniProt: A0ZZH6, sucrose phosphorylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1156 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 1000, 150MM NACL, MES pH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.51→45.506 Å / Num. obs: 175921 / % possible obs: 95 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.0806 / Net I/σ(I): 10.32
Reflection shellResolution: 1.51→1.564 Å / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 0.89

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→45.506 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.1
RfactorNum. reflection% reflection
Rfree0.1884 8566 4.88 %
Rwork0.1656 --
obs0.1667 175552 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.42 Å2 / Biso mean: 23.4546 Å2 / Biso min: 5.67 Å2
Refinement stepCycle: final / Resolution: 1.51→45.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7947 0 74 1156 9177
Biso mean--14.83 36.02 -
Num. residues----1011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088234
X-RAY DIFFRACTIONf_angle_d1.0611197
X-RAY DIFFRACTIONf_chiral_restr0.0451232
X-RAY DIFFRACTIONf_plane_restr0.0051464
X-RAY DIFFRACTIONf_dihedral_angle_d12.8492970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.52720.35782730.33145668594196
1.5272-1.54510.33152680.31915643591197
1.5451-1.5640.31792710.30485660593197
1.564-1.58380.31873020.29525624592697
1.5838-1.60460.30022970.27995583588096
1.6046-1.62660.31722750.27555544581995
1.6266-1.64980.2883170.26145443576093
1.6498-1.67450.27263000.25475424572494
1.6745-1.70060.28122910.25285715600697
1.7006-1.72850.2692870.24215687597497
1.7285-1.75830.26833110.23135669598097
1.7583-1.79030.22862950.21365648594397
1.7903-1.82470.24172630.20285652591596
1.8247-1.8620.242940.18915616591096
1.862-1.90250.20172600.17665608586895
1.9025-1.94670.18962950.1715556585195
1.9467-1.99540.19992750.16735486576194
1.9954-2.04930.20022700.16245420569092
2.0493-2.10970.19862760.15775355563191
2.1097-2.17770.16322820.14515635591796
2.1777-2.25560.15842690.14435636590596
2.2556-2.34590.16473260.14265604593096
2.3459-2.45260.17213140.14545638595296
2.4526-2.58190.17882840.1465617590195
2.5819-2.74370.18022900.14995509579993
2.7437-2.95550.18242750.14475301557689
2.9555-3.25280.16812580.14185476573491
3.2528-3.72330.15562890.13955596588594
3.7233-4.69030.13442910.12555569586092
4.6903-45.52690.1622680.15245404567286
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6781-0.16040.31060.4585-0.19791.20760.04010.025-0.065-0.0246-0.02560.01270.123-0.029-0.0220.1346-0.00120.00680.1234-0.00540.140710.0252-9.71774.186
20.872-0.0547-0.15380.6941-0.06911.70740.0095-0.04420.15710.0461-0.0123-0.0248-0.2365-0.1171-0.00330.16740.0435-0.00830.1358-0.00540.18292.699911.0264-2.0363
31.7554-0.8375-0.46342.00511.13651.93560.04810.17210.2661-0.2715-0.02640.0262-0.568-0.32390.07060.34940.1225-0.00960.26350.06710.2255-1.053218.1168-19.6895
40.6939-0.00360.2320.2421-0.14641.2825-0.0216-0.0291-0.1153-0.02710.01870.04420.2384-0.1194-0.01270.2075-0.01610.02350.1350.010.172621.2329-12.1786-35.4628
50.8832-0.0174-0.20040.42610.0131.8477-0.00480.0470.1274-0.0793-0.0085-0.0543-0.07740.17360.00540.1442-0.00150.01190.15930.03420.175539.06080.2115-28.6995
62.95720.8252-1.37251.7057-1.04893.30340.0698-0.27720.1830.0932-0.0982-0.0893-0.21430.53960.11850.1573-0.0268-0.01450.2917-0.00180.186545.8392.5669-10.5086
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 253 )B0 - 253
2X-RAY DIFFRACTION2chain 'B' and (resid 254 through 444 )B254 - 444
3X-RAY DIFFRACTION3chain 'B' and (resid 445 through 504 )B445 - 504
4X-RAY DIFFRACTION4chain 'A' and (resid 0 through 253 )A0 - 253
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 444 )A254 - 444
6X-RAY DIFFRACTION6chain 'A' and (resid 445 through 505 )A445 - 505

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