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- PDB-3ucq: Crystal structure of amylosucrase from Deinococcus geothermalis -

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Basic information

Entry
Database: PDB / ID: 3ucq
TitleCrystal structure of amylosucrase from Deinococcus geothermalis
ComponentsAmylosucrase
KeywordsTRANSFERASE / thermostability / amylose synthesis / sucrose isomerization / beta/alpha-barrel / Carbohydrate binding / glycoside hydrolase / glucosyltransferase
Function / homology
Function and homology information


amylosucrase activity / carbohydrate metabolic process
Similarity search - Function
Amylosucrase, catalytic domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Rna Polymerase Sigma Factor; Chain: A / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Amylosucrase, catalytic domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Rna Polymerase Sigma Factor; Chain: A / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesDeinococcus geothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsGuerin, F. / Pizzut-Serin, S. / Guillet, V. / Mourey, L. / Potocki-Veronese, G. / Remaud-Simeon, M. / Andre, I. / Tranier, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the Bacterium Deinococcus geothermalis.
Authors: Guerin, F. / Barbe, S. / Pizzut-Serin, S. / Potocki-Veronese, G. / Guieysse, D. / Guillet, V. / Monsan, P. / Mourey, L. / Remaud-Simeon, M. / Andre, I. / Tranier, S.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Amylosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,12415
Polymers73,8041
Non-polymers1,31914
Water10,845602
1
A: Amylosucrase
hetero molecules

A: Amylosucrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,24730
Polymers147,6092
Non-polymers2,63928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10200 Å2
ΔGint-17 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.316, 110.203, 115.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1030-

HOH

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Components

#1: Protein Amylosucrase


Mass: 73804.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis (bacteria) / Strain: DSM 11300 / Gene: dgas, Dgeo_0572 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q1J0W0, amylosucrase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M sodium acetate, 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 6, 2009
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.97→115.52 Å / Num. all: 45290 / Num. obs: 44959 / % possible obs: 99.27 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.97→2.08 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G5A

1g5a


Resolution: 1.97→33.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.01 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18751 2395 5.1 %RANDOM
Rwork0.14454 ---
all0.14676 45290 --
obs0.14676 47355 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2--0.23 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.97→33.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 86 602 5817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0215494
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9637477
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74822.174276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66215843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9071565
X-RAY DIFFRACTIONr_chiral_restr0.1480.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214320
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1391.53320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87825318
X-RAY DIFFRACTIONr_scbond_it3.12732174
X-RAY DIFFRACTIONr_scangle_it4.5434.52149
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 179 -
Rwork0.185 3179 -
obs-6837 96.94 %

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