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- PDB-3wq6: beta-Primeverosidase in complex with disaccharide substrate-analo... -

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Basic information

Entry
Database: PDB / ID: 3wq6
Titlebeta-Primeverosidase in complex with disaccharide substrate-analog N-beta-primeverosylamidine, artificial aglycone derivative
Componentsbeta-primeverosidase
KeywordsHYDROLASE / DIGLYCOSIDASE / DIGLYCOSIDE / DISACCHARIDE / GLYCOSIDE HYDROLASE FAMILY 1 (GH1) / (BETA/ALPHA)8 BARREL / SPECIFIC HYDROLYSIS OF BETA-PRIMEVEROSIDES / AROMA FORMATION / OOLONG TEA / BLACK TEA
Function / homology
Function and homology information


beta-primeverosidase / beta-primeverosidase activity / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-ZPA / Beta-primeverosidase
Similarity search - Component
Biological speciesCamellia sinensis (black tea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaino, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors.
Authors: Saino, H. / Shimizu, T. / Hiratake, J. / Nakatsu, T. / Kato, H. / Sakata, K. / Mizutani, M.
History
DepositionJan 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-primeverosidase
B: beta-primeverosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0098
Polymers114,2102
Non-polymers2,7996
Water32,0851781
1
A: beta-primeverosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8624
Polymers57,1051
Non-polymers1,7573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: beta-primeverosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1474
Polymers57,1051
Non-polymers1,0423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.112, 89.875, 195.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein beta-primeverosidase


Mass: 57104.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camellia sinensis (black tea) / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: Q7X9A9, beta-primeverosidase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 1783 molecules

#4: Chemical ChemComp-ZPA / 4-(N-benzylsuccinimide-3-sulfanyl)-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)butylamidine / 4-[(3R)-2,5-bis(oxidanylidene)-1-(phenylmethyl)pyrrolidin-3-yl]sulfanyl-N-[(2R,3R,4S,5S,6R)-3,4,5-tris(oxidanyl)-6-[[(2 S,3R,4S,5R)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]oxan-2-yl]butanimidamide


Mass: 599.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H37N3O11S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1781 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10mg/mL protein, 0.01% TritonX-100, 21% PEG 4000, 0.3M ammonium acetate, 0.1M sodium citrate (pH 5.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 2006
RadiationMonochromator: Confocal, Multilayer Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 97485 / % possible obs: 100 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.6 / Num. unique all: 14038 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CBG

1cbg


Resolution: 1.8→39.37 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 15.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 4867 5 %RANDOM
Rwork0.155 ---
obs0.1564 97396 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7595 0 187 1781 9563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058052
X-RAY DIFFRACTIONf_angle_d0.99810931
X-RAY DIFFRACTIONf_dihedral_angle_d11.7982835
X-RAY DIFFRACTIONf_chiral_restr0.0381144
X-RAY DIFFRACTIONf_plane_restr0.0041388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8-1.86440.23084740.19659113
1.8644-1.9390.22745110.17139117
1.939-2.02720.19164940.16089164
2.0272-2.13410.19644810.15999141
2.1341-2.26780.17724600.15169227
2.2678-2.44290.18025000.15429196
2.4429-2.68870.19874850.15689262
2.6887-3.07760.17434910.15789237
3.0776-3.87690.17194550.14279404
3.8769-39.3790.16375160.1489668

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