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- PDB-1fp9: STRUCTURE OF AMYLOMALTASE FROM THERMUS THERMOPHILUS HB8 IN SPACE ... -

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Basic information

Entry
Database: PDB / ID: 1fp9
TitleSTRUCTURE OF AMYLOMALTASE FROM THERMUS THERMOPHILUS HB8 IN SPACE GROUP C2
Components4-ALPHA-GLUCANOTRANSFERASE
KeywordsTRANSFERASE / alpha-amylase / glycosyl hydrolase / family 13 / glycosyltransferase / 4-alpha-glucanotransferase / D-enzyme / MalQ gene product / transglycosylation / amylose / crystal contacts
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-alpha-glucanotransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsUitdehaag, J.C.M. / Euverink, G.J. / van der Veen, B.A. / van der Maarel, M. / Dijkstra, B.W.
CitationJournal: To be Published
Title: Structure of the amylomaltase from Thermus thermophilus HB8 in space group C2
Authors: Uitdehaag, J.C.M. / Euverink, G.J. / van der Veen, B.A. / van der Maarel, M. / Dijkstra, B.W.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-ALPHA-GLUCANOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)57,2641
Polymers57,2641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.913, 52.445, 104.908
Angle α, β, γ (deg.)90.00, 96.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 4-ALPHA-GLUCANOTRANSFERASE / AMYLOMALTASE


Mass: 57263.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: O87172, 4-alpha-glucanotransferase

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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: 2.5 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 12% PEG 20000, 100 mM maleate buffer, 0.1% (w/v) maltotriose, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.1→52.2 Å / Num. all: 10520 / Num. obs: 10132 / % possible obs: 96.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.03 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.7
Reflection shellResolution: 3.1→3.17 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.24 / % possible all: 96.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FP8

1fp8


Resolution: 3.1→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh & Huber as implemented in CNS 1.0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 876 -random
Rwork0.239 ---
all0.252 10476 --
obs0.252 10095 96.3 %-
Solvent computationSolvent model: CNS
Displacement parametersBiso mean: 34.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-3.1 Å
Luzzati sigma a0.63 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 0 0 4062
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.03138
X-RAY DIFFRACTIONc_bond_d0.003938
X-RAY DIFFRACTIONc_dihedral_angle_d20.68967
X-RAY DIFFRACTIONc_improper_angle_d0.69523
X-RAY DIFFRACTIONc_mcbond_it2.455
X-RAY DIFFRACTIONc_mcangle_it2.944
X-RAY DIFFRACTIONc_scbond_it4.057
X-RAY DIFFRACTIONc_scangle_it5.237

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