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- PDB-2pwh: Crystal structure of the trehalulose synthase MutB from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 2pwh
TitleCrystal structure of the trehalulose synthase MutB from Pseudomonas mesoacidophila MX-45
ComponentsSucrose isomerase
KeywordsISOMERASE / trehalulose synthase / sucrose isomerase / alpha-amylase family / (beta/alpha)8 barrel
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
Biological speciesPseudomonas mesoacidophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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)127,7004
Polymers127,6192
Non-polymers802
Water27,3471518
1
A: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8502
Polymers63,8101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sucrose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8502
Polymers63,8101
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.580, 71.540, 81.750
Angle α, β, γ (deg.)67.66, 73.04, 70.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Sucrose isomerase


Mass: 63809.672 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, methylaspartate mutase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1518 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% 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: BM30A / Wavelength: 0.9803 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2005 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9803 Å / Relative weight: 1
ReflectionResolution: 2→19.6 Å / Num. all: 80624 / Num. obs: 80624 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 8.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.84 / Num. unique all: 10860 / Rsym value: 0.296

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1ZJA

1zja


Resolution: 2→19.56 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1748887.92 / 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
Rfree0.215 6503 8.1 %RANDOM
Rwork0.172 ---
obs0.172 80618 96.7 %-
all-80618 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.493 Å2 / ksol: 0.366204 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å2-4.38 Å2-4.99 Å2
2--0.38 Å25.28 Å2
3----3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9017 0 2 1518 10537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 1029 7.7 %
Rwork0.256 12315 -
obs--95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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