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- PDB-1uyp: The three-dimensional structure of beta-fructosidase (invertase) ... -

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Basic information

Entry
Database: PDB / ID: 1uyp
TitleThe three-dimensional structure of beta-fructosidase (invertase) from Thermotoga maritima
ComponentsBETA-FRUCTOSIDASE
KeywordsHYDROLASE / INVERTASE / GLYCOSYL HYDROLASE FAMILY 32 / SUCROSE DEGRADATION / BETA-PROPELLER
Function / homology
Function and homology information


beta-fructofuranosidase activity / beta-fructofuranosidase / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 ...Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Beta-fructosidase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsAlberto, F. / Bignon, C. / Sulzenbacher, G. / Henrissat, B. / Czjzek, M.
CitationJournal: J. Biol. Chem. / Year: 2004
Title: The three-dimensional structure of invertase (beta-fructosidase) from Thermotoga maritima reveals a bimodular arrangement and an evolutionary relationship between retaining and inverting glycosidases.
Authors: Alberto, F. / Bignon, C. / Sulzenbacher, G. / Henrissat, B. / Czjzek, M.
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
SupersessionMar 22, 2004ID: 1UTW
Revision 1.0Mar 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Refinement description
Category: citation / diffrn_radiation / refine
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol / _refine.pdbx_method_to_determine_struct
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: BETA-FRUCTOSIDASE
B: BETA-FRUCTOSIDASE
C: BETA-FRUCTOSIDASE
D: BETA-FRUCTOSIDASE
E: BETA-FRUCTOSIDASE
F: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,43028
Polymers299,3176
Non-polymers2,11322
Water31,6341756
1
A: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4827
Polymers49,8861
Non-polymers5956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3636
Polymers49,8861
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2665
Polymers49,8861
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9782
Polymers49,8861
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0743
Polymers49,8861
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: BETA-FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2665
Polymers49,8861
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.480, 114.670, 130.030
Angle α, β, γ (deg.)90.00, 98.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A17 - 28
2113B17 - 28
3113C17 - 28
4113D17 - 28
5113E17 - 28
6113F17 - 28
1213A31 - 39
2213B31 - 39
3213C31 - 39
4213D31 - 39
5213E31 - 39
6213F31 - 39
1313A49 - 55
2313B49 - 55
3313C49 - 55
4313D49 - 55
5313E49 - 55
6313F49 - 55
1413A62 - 68
2413B62 - 68
3413C62 - 68
4413D62 - 68
5413E62 - 68
6413F62 - 68
1513A75 - 85
2513B75 - 85
3513C75 - 85
4513D75 - 85
5513E75 - 85
6513F75 - 85
1613A88 - 94
2613B88 - 94
3613C88 - 94
4613D88 - 94
5613E88 - 94
6613F88 - 94
1713A106 - 114
2713B106 - 114
3713C106 - 114
4713D106 - 114
5713E106 - 114
6713F106 - 114
1813A120 - 133
2813B120 - 133
3813C120 - 133
4813D120 - 133
5813E120 - 133
6813F120 - 133
1913A137 - 148
2913B137 - 148
3913C137 - 148
4913D137 - 148
5913E137 - 148
6913F137 - 148
11013A151 - 160
21013B151 - 160
31013C151 - 160
41013D151 - 160
51013E151 - 160
61013F151 - 160
11113A164 - 172
21113B164 - 172
31113C164 - 172
41113D164 - 172
51113E164 - 172
61113F164 - 172
11213A178 - 187
21213B178 - 187
31213C178 - 187
41213D178 - 187
51213E178 - 187
61213F178 - 187
11313A194 - 201
21313B194 - 201
31313C194 - 201
41313D194 - 201
51313E194 - 201
61313F194 - 201
11413A204 - 211
21413B204 - 211
31413C204 - 211
41413D204 - 211
51413E204 - 211
61413F204 - 211
11513A216 - 224
21513B216 - 224
31513C216 - 224
41513D216 - 224
51513E216 - 224
61513F216 - 224
11613A229 - 236
21613B229 - 236
31613C229 - 236
41613D229 - 236
51613E229 - 236
61613F229 - 236
11713A244 - 248
21713B244 - 248
31713C244 - 248
41713D244 - 248
51713E244 - 248
61713F244 - 248
11813A255 - 260
21813B255 - 260
31813C255 - 260
41813D255 - 260
51813E255 - 260
61813F255 - 260
11913A285 - 290
21913B285 - 290
31913C285 - 290
41913D285 - 290
51913E285 - 290
61913F285 - 290
12013A293 - 298
22013B293 - 298
32013C293 - 298
42013D293 - 298
52013E293 - 298
62013F293 - 298
12113A306 - 313
22113B306 - 313
32113C306 - 313
42113D306 - 313
52113E306 - 313
62113F306 - 313
12213A317 - 320
22213B317 - 320
32213C317 - 320
42213D317 - 320
52213E317 - 320
62213F317 - 320
12313A328 - 343
22313B328 - 343
32313C328 - 343
42313D328 - 343
52313E328 - 343
62313F328 - 343
12413A348 - 354
22413B348 - 354
32413C348 - 354
42413D348 - 354
52413E348 - 354
62413F348 - 354
12513A357 - 361
22513B357 - 361
32513C357 - 361
42513D357 - 361
52513E357 - 361
62513F357 - 361
12613A362 - 376
22613B362 - 376
32613C362 - 376
42613D362 - 376
52613E362 - 376
62613F362 - 376
12713A386 - 390
22713B386 - 390
32713C386 - 390
42713D386 - 390
52713E386 - 390
62713F386 - 390
12813A393 - 398
22813B393 - 398
32813C393 - 398
42813D393 - 398
52813E393 - 398
62813F393 - 398
12913A402 - 407
22913B402 - 407
32913C402 - 407
42913D402 - 407
52913E402 - 407
62913F402 - 407
13013A416 - 432
23013B416 - 432
33013C416 - 432
43013D416 - 432
53013E416 - 432
63013F416 - 432

NCS oper:
IDCodeMatrixVector
1given(1, -0.000162, 0.000216), (0.000162, 1, -9.5E-5), (-0.000216, 9.5E-5, 1)-0.01542, 0.00795, 0.00113
2given(1, 0.000225, 0.000693), (-0.000226, 1, 0.000365), (-0.000693, -0.000365, 1)-0.01318, -0.01009, 0.00019
3given(1, -7.8E-5, -2.8E-5), (7.8E-5, 1, -0.00014), (2.8E-5, 0.00014, 1)-0.00112, -0.00564, -0.00032
4given(1, 0.000842, 0.000187), (-0.000842, 1, 0.000408), (-0.000186, -0.000408, 1)0.01214, -0.00274, -0.0048
5given(1, -8.4E-5, -0.000585), (8.5E-5, 1, 0.000412), (0.000585, -0.000412, 1)-0.03445, 0.02662, 0.0063

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
BETA-FRUCTOSIDASE


Mass: 49886.191 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM 3109) / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O33833, beta-fructofuranosidase

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Non-polymers , 5 types, 1778 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1756 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYSES HYDROLYSIS OF TERMINAL NON-REDUCING BETA-D- FRUCTOFURANOSIDE RESIDUES IN BETA-D-FRUCTOFURANOSIDES.

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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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growpH: 4.2
Details: 15 % PEG 1000, 150 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG10001drop
2150 mM1dropLi2SO4
3100 mMsodium citrate1droppH4.2
411 mg/mlprotein1drop
517 %PEG10001reservoir
650 mM1reservoirLi2SO4
71 %isopropanol1reservoir
8100 mMsodium citrate1reservoirpH4.2

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→34 Å / Num. obs: 184592 / % possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→129.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.695 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 10694 5 %RANDOM
Rwork0.177 ---
obs0.179 202520 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20.92 Å2
2---0.11 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21120 0 120 1756 22996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02121764
X-RAY DIFFRACTIONr_bond_other_d0.0030.0219114
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.94529453
X-RAY DIFFRACTIONr_angle_other_deg1.001344578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44852586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.23096
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0224126
X-RAY DIFFRACTIONr_gen_planes_other0.0090.024632
X-RAY DIFFRACTIONr_nbd_refined0.2180.23925
X-RAY DIFFRACTIONr_nbd_other0.2630.223750
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.213481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.21306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3490.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.277
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.2250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.266
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9681.512864
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.868220850
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.81538900
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5884.58603
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1538tight positional0.090.05
2B1538tight positional0.070.05
3C1538tight positional0.070.05
4D1538tight positional0.070.05
5E1538tight positional0.060.05
6F1538tight positional0.080.05
1A2395loose positional0.545
2B2395loose positional0.65
3C2395loose positional0.665
4D2395loose positional0.485
5E2395loose positional0.495
6F2395loose positional0.635
1A1538tight thermal0.20.5
2B1538tight thermal0.170.5
3C1538tight thermal0.190.5
4D1538tight thermal0.170.5
5E1538tight thermal0.160.5
6F1538tight thermal0.180.5
1A2395loose thermal1.6910
2B2395loose thermal1.510
3C2395loose thermal1.6210
4D2395loose thermal1.3810
5E2395loose thermal1.5410
6F2395loose thermal1.4710
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 706
Rwork0.27 13649
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.027
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.24

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