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- PDB-4h8v: Crystal structure of the trehalulose synthase MUTB in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4h8v
TitleCrystal structure of the trehalulose synthase MUTB in complex with trehalulose
ComponentsSucrose isomerase
KeywordsISOMERASE / NATIVE ENZYME / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING
Function / homology
Function and homology information


alpha-amylase activity / oligosaccharide catabolic process / isomerase activity / 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
1-O-alpha-D-glucopyranosyl-D-fructose / Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsLipski, A. / Ravaud, S. / 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 1.1Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.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_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,6426
Polymers127,8782
Non-polymers7654
Water21,2581180
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3213
Polymers63,9391
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3213
Polymers63,9391
Non-polymers3822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.27, 73.92, 82.96
Angle α, β, γ (deg.)66.07, 74.56, 72.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 63938.848 Da / Num. of mol.: 2 / Fragment: TREHALULOSE SYNTHASE MUTB, UNP residues 28-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: PHWG315 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q2PS28, UniProt: M1E1F6*PLUS, EC: 5.4.11.99
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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.: 2 / Source method: obtained synthetically / Formula: C12H22O11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1180 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG20000, 0.1M Na cacodylate, 0.01M L-cysteine, pH 6, 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: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→35.5 Å / Num. all: 95875 / Num. obs: 90958 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 1.95→2.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.16 / Num. unique all: 26719 / % possible all: 91.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1ZJA

1zja


Resolution: 1.95→35.5 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 4546 5 %RANDOM
Rwork0.1969 ---
obs0.1998 90940 95.1 %-
all-90940 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8983 0 48 1180 10211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079371
X-RAY DIFFRACTIONf_angle_d1.05112760
X-RAY DIFFRACTIONf_dihedral_angle_d13.3423392
X-RAY DIFFRACTIONf_chiral_restr0.0791303
X-RAY DIFFRACTIONf_plane_restr0.0051686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.97220.37551120.3117214172
1.9722-1.99540.34511510.289286794
1.9954-2.01970.34121520.2605287696
2.0197-2.04530.32141520.2648289796
2.0453-2.07220.30871540.2646292796
2.0722-2.10060.34291530.2504289596
2.1006-2.13060.2861510.229288196
2.1306-2.16240.26451540.242292096
2.1624-2.19620.4021440.3104273390
2.1962-2.23220.38611440.3436273389
2.2322-2.27070.47251500.3951284995
2.2707-2.31190.35921530.2798290896
2.3119-2.35640.30431520.2386289596
2.3564-2.40450.27311550.2141294897
2.4045-2.45680.30451540.204292896
2.4568-2.51390.26511540.2049291997
2.5139-2.57670.26431540.1911294897
2.5767-2.64640.27131530.1899290597
2.6464-2.72420.291540.1901292696
2.7242-2.81210.25711550.1829293297
2.8121-2.91260.24011540.1793294297
2.9126-3.02910.23041550.1801293697
3.0291-3.16690.28931540.182293496
3.1669-3.33380.22291540.1688292197
3.3338-3.54250.21791550.1675295297
3.5425-3.81570.22521530.1627290596
3.8157-4.19910.16081560.1272295098
4.1991-4.80550.15211550.1187295397
4.8055-6.04950.17361560.1287295497
6.0495-35.5170.17971530.1508291996

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