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- PDB-4h7v: MUTB inactive double mutant D200A-D415N in complex with GLUCOSE -

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Basic information

Entry
Database: PDB / ID: 4h7v
TitleMUTB inactive double mutant D200A-D415N in complex with GLUCOSE
ComponentsSucrose isomerase
KeywordsISOMERASE / ISOMALTULOSE SYNTHASE LIKE / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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_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 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,3207
Polymers127,7882
Non-polymers5335
Water19,8171100
1
A: 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
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2064
Polymers63,8941
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.7, 71.2, 85.4
Angle α, β, γ (deg.)118.1, 90.2, 109.7
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: D415N, D200A
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-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1100 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
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: ID29 / Wavelength: 0.98081 Å
DetectorType: PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98081 Å / Relative weight: 1
ReflectionResolution: 1.8→42.2 Å / Num. all: 113616 / Num. obs: 105583 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 22.97 Å2 / Rsym value: 0.103 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.4 / Num. unique all: 28403 / % possible all: 92.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZJB

1zjb


Resolution: 1.8→42.2 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 5278 5 %RANDOM
Rwork0.1713 ---
obs0.1737 105559 93.1 %-
all-105559 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8868 0 32 1100 10000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149250
X-RAY DIFFRACTIONf_angle_d1.5812609
X-RAY DIFFRACTIONf_dihedral_angle_d12.613307
X-RAY DIFFRACTIONf_chiral_restr0.1061294
X-RAY DIFFRACTIONf_plane_restr0.0091665
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 (%)
1.8-1.82050.2531800.197342193
1.8205-1.84190.2651750.1888332093
1.8419-1.86430.26731760.1934334192
1.8643-1.88790.24181730.1813328193
1.8879-1.91280.25581740.1774331593
1.9128-1.9390.23681760.186334091
1.939-1.96670.26561640.1839311689
1.9667-1.9960.2621810.1838344294
1.996-2.02720.21791770.1787336994
2.0272-2.06050.27121760.184334094
2.0605-2.0960.25991780.1774337494
2.096-2.13410.25431760.1746334993
2.1341-2.17510.23341760.1775334294
2.1751-2.21950.23921780.178338594
2.2195-2.26780.23321760.1696334793
2.2678-2.32050.21581770.1662336294
2.3205-2.37860.22121740.1633330093
2.3786-2.44290.2231770.1669335593
2.4429-2.51480.23591740.1727330892
2.5148-2.59590.22591770.1756336195
2.5959-2.68870.25181780.1743338394
2.6887-2.79630.21991780.1715339194
2.7963-2.92350.21181780.172337094
2.9235-3.07760.24521760.1782335293
3.0776-3.27040.18861750.1736332093
3.2704-3.52280.22511740.171330692
3.5228-3.87710.18221740.1626330292
3.8771-4.43760.17891760.1484334993
4.4376-5.58880.16921750.1547333493
5.5888-42.19740.20881790.1761340695

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