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- PDB-6s9u: Crystal structure of sucrose 6F-phosphate phosphorylase from Ilum... -

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Basic information

Entry
Database: PDB / ID: 6s9u
TitleCrystal structure of sucrose 6F-phosphate phosphorylase from Ilumatobacter coccineus
ComponentsPutative sucrose phosphorylase
KeywordsTRANSFERASE / Glycoside phosphorylase / sucrose 6-phosphate / glycoside hydrolase family GH13-18
Function / homologysucrose 6F-phosphate phosphorylase / Oligo-1,6-glucosidase, domain 2 / glycosyltransferase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / PHOSPHATE ION / Sucrose 6(F)-phosphate phosphorylase / Sucrose 6(F)-phosphate phosphorylase
Function and homology information
Biological speciesIlumatobacter coccineus YM16-304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsCapra, N. / Franceus, J. / Desmet, T. / Thunnissen, A.M.W.H.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Structural Comparison of a Promiscuous and a Highly Specific Sucrose 6 F -Phosphate Phosphorylase.
Authors: Franceus, J. / Capra, N. / Desmet, T. / Thunnissen, A.W.H.
History
DepositionJul 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 15, 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

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Assembly

Deposited unit
A: Putative sucrose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7495
Polymers59,9671
Non-polymers7824
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint3 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.434, 92.054, 179.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative sucrose phosphorylase


Mass: 59966.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ilumatobacter coccineus YM16-304 (bacteria)
Gene: YM304_32550 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: M5A566, UniProt: A0A6C7EEG6*PLUS, sucrose phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 200 mM Na/K phosphate, 100 mM Bis-Tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→46.03 Å / Num. obs: 33373 / % possible obs: 99.6 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.051 / Rrim(I) all: 0.118 / Net I/σ(I): 9.7 / Num. measured all: 169930 / Scaling rejects: 82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.115.10.8291305025670.6380.4050.9252.1100
8.94-46.034.30.04719834630.9970.0240.05422.598.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PHENIX1.14rc1_3161refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→46.027 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 19.46
RfactorNum. reflection% reflection
Rfree0.1997 1621 4.87 %
Rwork0.1657 --
obs0.1674 33317 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 32.9719 Å2 / Biso min: 14.41 Å2
Refinement stepCycle: final / Resolution: 2.05→46.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 115 313 4563
Biso mean--55.82 32.61 -
Num. residues----520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.11030.3221310.26912605100
2.1103-2.17850.23961440.22842619100
2.1785-2.25630.2151330.20622611100
2.2563-2.34670.21981280.19542648100
2.3467-2.45340.21531220.1834258198
2.4534-2.58280.23431320.1827255297
2.5828-2.74460.20241310.17672637100
2.7446-2.95650.21211350.17632661100
2.9565-3.25390.20661250.16272644100
3.2539-3.72460.18241310.14952690100
3.7246-4.69190.1511460.122680100
4.6919-460.19651630.1554276899
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)
10.5397-0.49760.34761.7774-0.67691.49540.01870.02010.025-0.0731-0.0354-0.00640.0109-0.09040.01370.1575-0.0059-0.00090.1987-0.010.191915.908436.729755.1069
21.17210.05460.12130.864-0.29951.5392-0.0198-0.04140.04790.044-0.0143-0.0341-0.02320.03860.02820.20060.0165-0.00920.216-0.00720.211826.714829.312977.6997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 257 )A5 - 257
2X-RAY DIFFRACTION2chain 'A' and (resid 258 through 524 )A258 - 524

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