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- PDB-2pwd: Crystal Structure of the Trehalulose Synthase MUTB from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 2pwd
TitleCrystal Structure of the Trehalulose Synthase MUTB from Pseudomonas Mesoacidophila MX-45 Complexed to the Inhibitor Deoxynojirmycin
ComponentsSucrose isomerase
KeywordsISOMERASE / TREHALULOSE SYNTHASE / SUCROSE ISOMERASE / ALPHA-AMYLASE FAMILY / (BETA/ALPHA)8 BARREL
Function / homology
Function and homology information


oligosaccharide catabolic process / alpha-amylase activity / 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
1-DEOXYNOJIRIMYCIN / 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: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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)128,2846
Polymers127,8782
Non-polymers4074
Water27,2931515
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1423
Polymers63,9391
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1423
Polymers63,9391
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.400, 72.000, 82.000
Angle α, β, γ (deg.)67.20, 73.40, 70.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sucrose isomerase


Mass: 63938.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mesoacidophila (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: PHWG315 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2PS28, isomaltulose synthase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1515 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG20000, 0.1M Na cacodylate, 0.01M L-cysteine, pH 6, 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→42.3 Å / Num. all: 110212 / Num. obs: 110212 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 9.8 Å2 / Rsym value: 0.086 / Net I/σ(I): 9.72
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.92 / Num. unique all: 16151 / Rsym value: 0.27

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Processing

Software
NameVersionClassification
CNS1.1refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1ZJA

1zja


Resolution: 1.8→42.32 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1675716.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 5570 5.1 %RANDOM
Rwork0.169 ---
obs0.169 110211 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.829 Å2 / ksol: 0.37791 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-3.94 Å2-1.21 Å2
2--2.32 Å22.54 Å2
3----2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8935 0 24 1515 10474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 912 5.1 %
Rwork0.244 17119 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5noj.paramnoj.top

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