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- PDB-2pwf: Crystal structure of the MutB D200A mutant in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 2pwf
TitleCrystal structure of the MutB D200A mutant in complex with glucose
ComponentsSucrose isomerase
KeywordsISOMERASE / TREHALULOSE SYNTHASE / SUCROSE ISOMERASE / ALPHA-AMYLASE FAMILY / (BETA/ALPHA)8 / BARREL / enzyme complex
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
beta-D-glucopyranose / Sucrose isomerase
Similarity search - Component
Biological speciesPseudomonas mesoacidophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsRavaud, S. / Robert, X. / Haser, R. / Aghajari, N.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization.
Authors: Ravaud, S. / Robert, X. / Watzlawick, H. / Haser, R. / Mattes, R. / Aghajari, N.
History
DepositionMay 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)255,94412
Polymers255,0634
Non-polymers8818
Water57,4863191
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9863
Polymers63,7661
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9863
Polymers63,7661
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9863
Polymers63,7661
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9863
Polymers63,7661
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.980, 85.810, 122.140
Angle α, β, γ (deg.)81.77, 81.43, 89.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Sucrose isomerase


Mass: 63765.664 Da / Num. of mol.: 4 / Mutation: D200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mesoacidophila (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: pHWG678.6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2PS28, isomaltulose synthase
#2: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 3191 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13%PEG20000, 0.1M Hepes, 0.01M L-cysteine, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→45.8 Å / Num. all: 225077 / Num. obs: 225077 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.86
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.08 / Num. unique all: 33321 / Rsym value: 0.279

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Processing

Software
NameVersionClassification
CNS1.1refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→45.85 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2501102.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 11212 5 %RANDOM
Rwork0.198 ---
obs0.198 225058 95.3 %-
all-225077 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.2434 Å2 / ksol: 0.373698 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20.18 Å22 Å2
2---2.95 Å2-0.5 Å2
3---3.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17902 0 52 3191 21145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 1860 5 %
Rwork0.267 35265 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top

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