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- PDB-4gi6: Crystal structure of the MUTB F164L mutant in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 4gi6
TitleCrystal structure of the MUTB F164L mutant in complex with glucose
ComponentsSucrose isomerase
KeywordsISOMERASE / Enzyme complex / 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
alpha-D-glucopyranose / Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsLipski, A. / Haser, R. / Aghajari, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity
Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Rhimi, M. / Haser, R. / Mattes, R. / Aghajari, N.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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)128,92914
Polymers127,8102
Non-polymers1,11912
Water16,069892
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4016
Polymers63,9051
Non-polymers4975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5288
Polymers63,9051
Non-polymers6237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.9, 86.3, 118.3
Angle α, β, γ (deg.)90.00, 97.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Sucrose isomerase / Trehalulose synthase


Mass: 63904.832 Da / Num. of mol.: 2 / Fragment: MUTB fragment, UNP residues 28-584 / Mutation: F164L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: PHWG660.12 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q2PS28, UniProt: M1E1F3*PLUS, EC: 5.4.11.99
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 903 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 12%(w/v) PEG20000, 0.01M L-Cysteine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97559 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2008
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97559 Å / Relative weight: 1
ReflectionResolution: 2.15→15 Å / Num. all: 69351 / Num. obs: 68858 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.117 / Net I/σ(I): 9.4
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.3 / Num. unique all: 12519 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1ZJB

1zjb


Resolution: 2.15→14.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.89 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.232 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3477 5 %RANDOM
Rwork0.169 ---
obs0.172 65380 99.3 %-
all-65380 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-1.75 Å2
2---1.31 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.15→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8914 0 70 892 9876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199326
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.93812693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08751127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01223.657484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.843151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5471563
X-RAY DIFFRACTIONr_chiral_restr0.1050.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217414
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 232 -
Rwork0.231 4844 -
obs-100 99.57 %

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