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- PDB-4h8u: MUTB inactive double mutant D200A-D415N soaked with sucrose and h... -

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Basic information

Entry
Database: PDB / ID: 4h8u
TitleMUTB inactive double mutant D200A-D415N soaked with sucrose and having as bound ligands sucrose in molecule A and the reaction product trehalulose in molecule B
ComponentsSucrose isomerase
KeywordsISOMERASE / ISOMALTULOSE SYNTHASE LIKE INACTIVE MUTANT / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING
Function / homology
Function and homology information


isomerase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Glycosyl hydrolase, C-terminal (DUF3459) / Domain of unknown function (DUF3459) / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
sucrose / 1-O-alpha-D-glucopyranosyl-D-fructose / Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLipski, A. / Haser, R. / Aghajari, N.
CitationJournal: To be Published
Title: Insights into product binding in sucrose isomerases from crystal structures of MutB from Rhizobium sp.
Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Haser, R. / Mattes, R. / Aghajari, N.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrose isomerase
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6457
Polymers127,7882
Non-polymers8575
Water26,2481457
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3684
Polymers63,8941
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2763
Polymers63,8941
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.37, 73.68, 82.67
Angle α, β, γ (deg.)66.15, 74.29, 72.42
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 63893.855 Da / Num. of mol.: 2 / Fragment: TREHALULOSE SYNTHASE MUTB, UNP residues 28-584 / Mutation: D200A, D415N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: pHWG800.2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q2PS28, UniProt: M1E1F6*PLUS, EC: 5.4.11.99

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-TEU / 1-O-alpha-D-glucopyranosyl-D-fructose / 1-O-alpha-D-glucosyl-D-fructose / 1-O-D-glucosyl-D-fructose / 1-O-glucosyl-D-fructose


Type: D-saccharide / Mass: 342.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O11

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Non-polymers , 3 types, 1460 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1457 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG10000, 0.1M TRIS-HCL , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2010
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→38.4 Å / Num. all: 88374 / Num. obs: 83253 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 22.19 Å2 / Rsym value: 0.084 / Net I/σ(I): 9
Reflection shellResolution: 2→2.2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.69 / Num. unique all: 20684 / % possible all: 94.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PWH

2pwh


Resolution: 2→38.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / SU B: 5.163 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.209 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 4163 5 %RANDOM
Rwork0.1887 ---
obs0.1922 79088 94.39 %-
all-79088 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-1.4 Å2-0.64 Å2
2--0.07 Å21.37 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8923 0 54 1457 10434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199352
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.93812751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56351134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96623.612490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.863151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2621564
X-RAY DIFFRACTIONr_chiral_restr0.1210.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217462
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 307 -
Rwork0.255 5838 -
obs--94.23 %

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