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- PDB-1w2t: beta-fructosidase from Thermotoga maritima in complex with raffinose -

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Basic information

Entry
Database: PDB / ID: 1w2t
Titlebeta-fructosidase from Thermotoga maritima in complex with raffinose
ComponentsBETA FRUCTOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE / INVERTASE / RAFFINOSE / BETA FRUCTOSIDASE
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 / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsAlberto, F. / Henrissat, B. / Czjzek, M.
CitationJournal: Biochem.J. / Year: 2006
Title: Crystal Structure of Inactivated Thermotoga Maritima Invertase in Complex with the Trisaccharide Substrate Raffinose.
Authors: Alberto, F. / Jordi, E. / Henrissat, B. / Czjzek, M.
History
DepositionJul 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
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)302,83617
Polymers299,2336
Non-polymers3,60311
Water34,0121888
1
A: BETA FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5693
Polymers49,8721
Non-polymers6972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BETA FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4733
Polymers49,8721
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BETA FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5694
Polymers49,8721
Non-polymers6973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BETA FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3772
Polymers49,8721
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: BETA FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4733
Polymers49,8721
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: BETA FRUCTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3772
Polymers49,8721
Non-polymers5041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.500, 114.700, 130.000
Angle α, β, γ (deg.)90.00, 98.90, 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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 1 - 432 / Label seq-ID: 1 - 432

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(0.43221, -0.7589, -0.4871), (0.74277, -0.00671, 0.66952), (0.51136, -0.65118, 0.56078)31.76897, 42.67206, -58.00331
2given(-0.24284, 0.70156, 0.66996), (0.76502, -0.28615, 0.57694), (0.59647, 0.65264, -0.46722)-20.84123, 36.52012, -11.14813
3given(-0.08826, -0.64016, 0.76316), (-0.64635, -0.54615, -0.53287), (0.75792, -0.54029, -0.36556)-36.24844, 0.09379, 43.93799
4given(-0.06164, 0.46446, -0.88345), (-0.39874, -0.82289, -0.4048), (-0.91499, 0.32731, 0.23592)19.65075, -1.72256, 5.84769
5given(-0.96583, -0.24709, 0.07817), (-0.25599, 0.95662, -0.13913), (-0.0404, -0.15438, -0.98719)-16.36945, -7.8308, 64.92795

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Components

#1: Protein
BETA FRUCTOSIDASE / SUCRASE / INVERTASE


Mass: 49872.168 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8
Description: STRAIN MSB8 (DSM 3109) KINDLY PROVIDED BY DR. W. LIEBL
Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O33833, beta-fructofuranosidase
#2: Polysaccharide
beta-D-fructofuranose-(2-1)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DFrufb2-1[DGalpa1-6]DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1888 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A-F ENGINEERED MUTATION GLU 190 ASP

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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: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: HANGING DROP TECHNIQUE 10% PEG 1000, 50 MM LI2SO4, 100 MM CITRATE PHOSPHATE BUFFER PH 4.2, CONCENTRATION PROTEIN 8 MG/ML, INCUBATION TEMPERATURE 20 C

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.87→129.099 Å / Num. obs: 225700 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 6
Reflection shellResolution: 1.87→30 Å / Redundancy: 3 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 3.9 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UYP

1uyp


Resolution: 1.87→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.25 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 11055 5 %RANDOM
Rwork0.198 ---
obs0.199 209387 97.7 %-
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: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å21.14 Å2
2---0.64 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.87→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21109 0 237 1888 23234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02121902
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219200
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.95329654
X-RAY DIFFRACTIONr_angle_other_deg0.854344788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48452581
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_restr0.0740.23172
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0224091
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024627
X-RAY DIFFRACTIONr_nbd_refined0.1830.23621
X-RAY DIFFRACTIONr_nbd_other0.2330.222966
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.213194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.21396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.273
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.2256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.50.287
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.512855
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.792220829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.04439047
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7294.58825
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
1A2521medium positional0.290.5
2B2521medium positional0.210.5
3C2521medium positional0.230.5
4D2521medium positional0.20.5
5E2521medium positional0.20.5
6F2521medium positional0.180.5
1A4111loose positional0.695
2B4111loose positional0.555
3C4111loose positional0.585
4D4111loose positional0.555
5E4111loose positional0.485
6F4111loose positional0.555
1A2521medium thermal0.462
2B2521medium thermal0.562
3C2521medium thermal0.432
4D2521medium thermal0.362
5E2521medium thermal0.32
6F2521medium thermal0.322
1A4111loose thermal1.0610
2B4111loose thermal110
3C4111loose thermal0.8310
4D4111loose thermal0.810
5E4111loose thermal0.6310
6F4111loose thermal0.6910
LS refinement shellResolution: 1.87→1.92 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.261 772
Rwork0.217 14259

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