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- PDB-4ha1: MutB inactive double mutant D200A-D415N in complex with isomaltulose -

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Basic information

Entry
Database: PDB / ID: 4ha1
TitleMutB inactive double mutant D200A-D415N in complex with isomaltulose
ComponentsSucrose isomerase
KeywordsISOMERASE / ISOMALTULOSE SYNTHASE LIKE / 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
alpha-D-glucopyranose / 6-O-alpha-D-glucopyranosyl-D-fructose / Sucrose isomerase / Sucrose isomerase
Similarity search - Component
Biological speciesRhizobium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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 25, 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / 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: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _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_auth_seq_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 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)128,3906
Polymers127,7882
Non-polymers6034
Water20,9331162
1
A: 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
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1143
Polymers63,8941
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.600, 73.350, 82.640
Angle α, β, γ (deg.)66.55, 73.86, 71.86
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-ISL / 6-O-alpha-D-glucopyranosyl-D-fructose / 6-O-alpha-D-glucosyl-D-fructose / 6-O-D-glucosyl-D-fructose / 6-O-glucosyl-D-fructose / Isomaltulose


Type: D-saccharide / Mass: 342.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H22O11
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→43.4 Å / Num. all: 66205 / Num. obs: 64580 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 24.39 Å2 / Rsym value: 0.165 / Net I/σ(I): 8.49
Reflection shellResolution: 2.2→2.5 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.95 / % possible all: 97.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5refinement
PHENIX1.8-1069refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PWH

2pwh


Resolution: 2.2→43.36 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.873 / SU ML: 0.28 / σ(F): 1.99 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 3228 5 %
Rwork0.1916 --
obs0.1946 64565 97.72 %
all-61351 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å2-2.82 Å2-0.92 Å2
2---0.37 Å22.64 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8907 0 37 1162 10106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049302
X-RAY DIFFRACTIONf_angle_d0.76312683
X-RAY DIFFRACTIONf_dihedral_angle_d12.253346
X-RAY DIFFRACTIONf_chiral_restr0.0571303
X-RAY DIFFRACTIONf_plane_restr0.0041676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23270.31771400.22612660X-RAY DIFFRACTION97
2.2327-2.26760.26381350.21382563X-RAY DIFFRACTION97
2.2676-2.30480.31091410.20942683X-RAY DIFFRACTION97
2.3048-2.34450.30351380.20672636X-RAY DIFFRACTION97
2.3445-2.38710.25821430.20372715X-RAY DIFFRACTION97
2.3871-2.4330.27271390.19542627X-RAY DIFFRACTION97
2.433-2.48270.25481400.1982668X-RAY DIFFRACTION97
2.4827-2.53670.26621400.20192651X-RAY DIFFRACTION97
2.5367-2.59570.29451390.19962657X-RAY DIFFRACTION98
2.5957-2.66060.30161400.20472653X-RAY DIFFRACTION98
2.6606-2.73250.28681400.20472658X-RAY DIFFRACTION98
2.7325-2.81290.28811430.19262720X-RAY DIFFRACTION98
2.8129-2.90370.2981400.19952654X-RAY DIFFRACTION98
2.9037-3.00740.26551390.19872635X-RAY DIFFRACTION98
3.0074-3.12780.2971410.20542683X-RAY DIFFRACTION98
3.1278-3.27010.27021410.19522682X-RAY DIFFRACTION98
3.2701-3.44240.23381420.19112698X-RAY DIFFRACTION98
3.4424-3.6580.231390.17862643X-RAY DIFFRACTION98
3.658-3.94030.19741410.17052689X-RAY DIFFRACTION98
3.9403-4.33650.22441430.16072702X-RAY DIFFRACTION98
4.3365-4.96320.20321420.16912693X-RAY DIFFRACTION98
4.9632-6.25010.21771410.18672684X-RAY DIFFRACTION99
6.2501-43.36830.1971410.20312683X-RAY DIFFRACTION98

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