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- PDB-1gju: Maltosyltransferase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1gju
TitleMaltosyltransferase from Thermotoga maritima
ComponentsMALTODEXTRIN GLYCOSYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA-AMYLASE / MALTOSYLTRANSFERASE
Function / homology
Function and homology information


transferase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF1923 / Domain of unknown function (DUF1923) / 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 ...Domain of unknown function DUF1923 / Domain of unknown function (DUF1923) / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Maltodextrin glycosyltransferase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsRoujeinikova, A. / Raasch, C. / Burke, J. / Baker, P.J. / Liebl, W. / Rice, D.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The Crystal Structure of Thermotoga Maritima Maltosyltransferase and its Implications for the Molecular Basis of the Novel Transfer Specificity
Authors: Roujeinikova, A. / Raasch, C. / Burke, J. / Baker, P.J. / Liebl, W. / Rice, D.W.
History
DepositionAug 2, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description
Category: atom_site / pdbx_database_proc ...atom_site / pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALTODEXTRIN GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0904
Polymers73,8051
Non-polymers2853
Water4,666259
1
A: MALTODEXTRIN GLYCOSYLTRANSFERASE
hetero molecules

A: MALTODEXTRIN GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,1798
Polymers147,6092
Non-polymers5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)148.740, 148.740, 106.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein MALTODEXTRIN GLYCOSYLTRANSFERASE


Mass: 73804.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 / References: UniProt: O33838
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 66 %
Crystal growpH: 4.8 / Details: 0.35-0.40 M AMMONIUM PHOSPHATE,, pH 4.80
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: Burke, J., (2000) Acta Crystallog., D56, 1049.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
2150 mM1dropNaCl
318 mg/mlprotein1drop
40.35-0.40 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 47952 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.9
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 9.9 / % possible all: 98
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 198549
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2369 5 %RANDOM
Rwork0.208 ---
obs0.208 46904 98.3 %-
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--6.085 Å20 Å20 Å2
2---6.085 Å20 Å2
3---12.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 15 259 5483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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