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- PDB-4gi8: Crystal structure of the MUTB F164L mutant from crystals soaked w... -

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Basic information

Entry
Database: PDB / ID: 4gi8
TitleCrystal structure of the MUTB F164L mutant from crystals soaked with the substrate sucrose
ComponentsSucrose isomerase
KeywordsISOMERASE / MUTANT 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
Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)129,30119
Polymers127,8102
Non-polymers1,49217
Water18,8081044
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,71210
Polymers63,9051
Non-polymers8079
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5909
Polymers63,9051
Non-polymers6858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.14, 86.11, 118.10
Angle α, β, γ (deg.)90.00, 97.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1044 / 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: 51.34 %
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: 1.95→48.92 Å / Num. all: 92762 / Num. obs: 91853 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.41 % / Biso Wilson estimate: 24.03 Å2 / Rsym value: 0.124 / Net I/σ(I): 11.74
Reflection shellResolution: 1.95→2.1 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 4.02 / Num. unique all: 17461 / % possible all: 95.2

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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: 1.95→48.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.962 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4596 5 %RANDOM
Rwork0.157 ---
obs0.158 87257 99.45 %-
all-87257 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-1.06 Å2
2---0.63 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8904 0 94 1044 10042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199469
X-RAY DIFFRACTIONr_angle_refined_deg1.431.93912892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70351152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07923.649485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.499151437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3631563
X-RAY DIFFRACTIONr_chiral_restr0.1040.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217537
LS refinement shellResolution: 1.95→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 311 -
Rwork0.229 5990 -
obs--92.87 %

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