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- PDB-6s9v: Crystal structure of sucrose 6F-phosphate phosphorylase from Ther... -

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Basic information

Entry
Database: PDB / ID: 6s9v
TitleCrystal structure of sucrose 6F-phosphate phosphorylase from Thermoanaerobacter thermosaccharolyticum
ComponentsSucrose 6(F)-phosphate phosphorylase
KeywordsTRANSFERASE / Glycoside phosphorylase / sucrose 6-phosphate / glycoside hydrolase family GH13-18
Function / homology
Function and homology information


sucrose 6F-phosphate phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / hexosyltransferase activity / carbohydrate metabolic process
Similarity search - Function
Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Sucrose 6(F)-phosphate phosphorylase
Similarity search - Component
Biological speciesThermoanaerobacterium thermosaccharolyticum DSM 571 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrose 6(F)-phosphate phosphorylase
B: Sucrose 6(F)-phosphate phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,73120
Polymers116,5932
Non-polymers2,13818
Water8,359464
1
A: Sucrose 6(F)-phosphate phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3649
Polymers58,2961
Non-polymers1,0688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sucrose 6(F)-phosphate phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,36611
Polymers58,2961
Non-polymers1,07010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.332, 83.690, 147.401
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11 through 35 or resid 37...
21(chain B and (resid 11 through 35 or resid 37...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYS(chain A and (resid 11 through 35 or resid 37...AA11 - 3511 - 35
12LEULEUTYRTYR(chain A and (resid 11 through 35 or resid 37...AA37 - 7137 - 71
13GLUGLUARGARG(chain A and (resid 11 through 35 or resid 37...AA73 - 10573 - 105
14HISHISVALVAL(chain A and (resid 11 through 35 or resid 37...AA7 - 5027 - 502
15GLUGLUHISHIS(chain A and (resid 11 through 35 or resid 37...AA143 - 254143 - 254
16GLNGLNVALVAL(chain A and (resid 11 through 35 or resid 37...AA256 - 502256 - 502
21GLYGLYLYSLYS(chain B and (resid 11 through 35 or resid 37...BB11 - 3511 - 35
22LEULEUTYRTYR(chain B and (resid 11 through 35 or resid 37...BB37 - 7137 - 71
23GLUGLUARGARG(chain B and (resid 11 through 35 or resid 37...BB73 - 10573 - 105
24ILEILEASPASP(chain B and (resid 11 through 35 or resid 37...BB107 - 141107 - 141
25GLUGLUHISHIS(chain B and (resid 11 through 35 or resid 37...BB143 - 254143 - 254
26GLNGLNTYRTYR(chain B and (resid 11 through 35 or resid 37...BB256 - 345256 - 345
27GLUGLUVALVAL(chain B and (resid 11 through 35 or resid 37...BB352 - 502352 - 502

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sucrose 6(F)-phosphate phosphorylase / Sucrose 6'-phosphate phosphorylase / SPP


Mass: 58296.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum DSM 571 (bacteria)
Gene: spp, Tthe_1921 / Variant: ATCC 7956 / DSM 571 / NCIB 9385 / NCA 3814 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: D9TT09, sucrose 6F-phosphate phosphorylase

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Non-polymers , 5 types, 482 molecules

#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#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.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 26% PEG 3350, 100 mM ammonium sulphate, 100 mM Bis-Tris propane buffer

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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: 1.83→45.37 Å / Num. obs: 86925 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.034 / Rrim(I) all: 0.081 / Net I/σ(I): 12.7 / Num. measured all: 461327
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
1.83-1.865.50.6712422944070.8010.3040.7392.399.8
9.85-45.374.70.04428556090.9970.0210.04927.396.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14rc1_3161refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R7A

1r7a


Resolution: 1.83→39.666 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 16.64
RfactorNum. reflection% reflection
Rfree0.1841 4255 4.9 %
Rwork0.1557 --
obs0.157 86839 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.38 Å2 / Biso mean: 35.0989 Å2 / Biso min: 14.92 Å2
Refinement stepCycle: final / Resolution: 1.83→39.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8054 0 180 464 8698
Biso mean--56.22 33.93 -
Num. residues----982
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4714X-RAY DIFFRACTION6.311TORSIONAL
12B4714X-RAY DIFFRACTION6.311TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.85080.28041690.2962699100
1.8508-1.87260.27671340.26192709100
1.8726-1.89540.2881480.24652702100
1.8954-1.91940.25371600.22692691100
1.9194-1.94470.25781600.20962719100
1.9447-1.97130.21861300.19762739100
1.9713-1.99950.21091460.17462700100
1.9995-2.02930.21281490.16852733100
2.0293-2.0610.19181330.17072736100
2.061-2.09480.19531550.17022747100
2.0948-2.13090.20171200.16892732100
2.1309-2.16970.1851290.16782745100
2.1697-2.21140.18511450.15542729100
2.2114-2.25650.18311400.15252747100
2.2565-2.30560.18611490.15342703100
2.3056-2.35920.1641470.14682731100
2.3592-2.41820.151560.142271899
2.4182-2.48360.17631560.149269599
2.4836-2.55660.22551490.1489273599
2.5566-2.63910.19491460.15162734100
2.6391-2.73350.17281390.15272748100
2.7335-2.84290.171270.14842773100
2.8429-2.97220.18241410.15612779100
2.9722-3.12890.18261280.15212786100
3.1289-3.32480.19621310.15632791100
3.3248-3.58130.16491410.14052779100
3.5813-3.94150.16241370.1312813100
3.9415-4.51110.1471310.12072821100
4.5111-5.68090.16251260.13642885100
5.6809-390.19951330.1912296599
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)
10.3924-0.1451-0.02251.17590.03070.46220.0066-0.0497-0.01730.14530.0153-0.0230.04410.0827-0.02830.20010.0083-0.0120.217-0.0040.164539.42772.972217.9765
21.0677-0.85240.0672.4725-0.16831.43050.08450.02980.1836-0.2159-0.0312-0.1052-0.31830.0616-0.03810.246-0.01990.03280.19320.00580.197339.467294.15027.1545
31.0152-0.0231-0.11780.58950.06330.80520.01020.10660.0653-0.1350.03540.00040.0223-0.0361-0.03840.21220.00330.00430.21810.01270.169234.913170.3573-2.9384
41.5137-0.39-0.40541.52690.41241.4572-0.00930.0429-0.208-0.0016-0.00820.05360.1896-0.02360.02070.2049-0.0248-0.00820.18950.01640.176533.480255.95056.4206
52.5622-0.0128-0.76931.20310.1360.61380.15160.37080.335-0.1282-0.09510.1117-0.1346-0.1458-0.04080.17550.0448-0.00940.19380.01180.17737.483598.285522.2431
62.3311-0.2826-0.41311.04820.17291.32350.15490.17750.2709-0.0937-0.01970.0314-0.16950.0038-0.12140.22230.01930.02780.18690.00730.20724.1172100.673224.0135
71.52260.01510.11341.45210.16861.55770.0892-0.0799-0.02370.1027-0.0154-0.1360.06940.1565-0.05670.1625-0.0027-0.01720.177-0.02570.158136.751593.352342.1198
82.125-0.26990.42891.0896-0.20991.75920.0431-0.15380.26930.0045-0.0214-0.0578-0.11820.0485-0.02630.2027-0.01420.02320.2033-0.04430.235925.5237100.904536.7779
92.08090.5824-0.22282.8176-0.13131.78280.0266-0.17470.5265-0.04180.0884-0.2494-0.10160.1167-0.06960.20940.02570.02360.227-0.07890.373216.7348107.823440.0071
102.0655-0.58670.17881.06220.23211.0871-0.0277-0.1887-0.10120.07810.00290.14530.0111-0.05280.02570.1848-0.00130.01150.1841-0.01030.19682.242794.440544.8567
112.1953-0.3373-0.3531.73140.32951.3218-0.0134-0.1886-0.2930.2359-0.01190.04720.12480.08650.0130.2052-0.00870.00960.15820.01130.24124.240982.439641.6378
121.5693-0.3813-0.48331.2190.33881.81960.05850.3243-0.1834-0.1352-0.0920.05120.09330.02250.0350.18110.0153-0.02040.2068-0.050.2281.757387.025724.9018
132.5615-0.18610.31622.20150.18671.5659-0.0792-0.04150.01340.02610.03480.287-0.1381-0.2450.01140.18150.02340.00990.2329-0.04630.3142-17.510997.744837.2315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 89 )A7 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 229 )A90 - 229
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 384 )A230 - 384
4X-RAY DIFFRACTION4chain 'A' and (resid 385 through 502 )A385 - 502
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 65 )B11 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 118 )B66 - 118
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 163 )B119 - 163
8X-RAY DIFFRACTION8chain 'B' and (resid 164 through 229 )B164 - 229
9X-RAY DIFFRACTION9chain 'B' and (resid 230 through 256 )B230 - 256
10X-RAY DIFFRACTION10chain 'B' and (resid 257 through 323 )B257 - 323
11X-RAY DIFFRACTION11chain 'B' and (resid 324 through 384 )B324 - 384
12X-RAY DIFFRACTION12chain 'B' and (resid 385 through 446 )B385 - 446
13X-RAY DIFFRACTION13chain 'B' and (resid 447 through 502 )B447 - 502

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