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- PDB-1lwj: CRYSTAL STRUCTURE OF T. MARITIMA 4-ALPHA-GLUCANOTRANSFERASE/ACARB... -

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Basic information

Entry
Database: PDB / ID: 1lwj
TitleCRYSTAL STRUCTURE OF T. MARITIMA 4-ALPHA-GLUCANOTRANSFERASE/ACARBOSE COMPLEX
Components4-ALPHA-GLUCANOTRANSFERASE
KeywordsTRANSFERASE / 4-alpha-glucanotransferase / alpha-amylase family / Thermotoga maritima / acarbose / (beta/alpha)8 barrel
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / oligosaccharide catabolic process / alpha-amylase activity / metal ion binding / cytoplasm
Similarity search - Function
4-alpha-glucanotransferase, C-terminal / 4-alpha-glucanotransferase, C-terminal / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...4-alpha-glucanotransferase, C-terminal / 4-alpha-glucanotransferase, C-terminal / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase / 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
MODIFIED ACARBOSE PENTASACCHARIDE / 4-alpha-glucanotransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoujeinikova, A. / Raasch, C. / Sedelnikova, S. / Liebl, W. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA 4-ALPHA-GLUCANOTRANSFERASE AND ITS ACARBOSE COMPLEX: IMPLICATIONS FOR SUBSTRATE SPECIFICITY AND CATALYSIS
Authors: Roujeinikova, A. / Raasch, C. / Sedelnikova, S. / Liebl, W. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDIES ON 4-ALPHA-GLUCANOTRANSFERASE FROM THERMOTOGA MARITIMA
Authors: Roujeinikova, A. / Raasch, C. / Sedelnikova, S. / Liebl, W. / Rice, D.W.
History
DepositionMay 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: 4-ALPHA-GLUCANOTRANSFERASE
B: 4-ALPHA-GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5156
Polymers103,8522
Non-polymers1,6644
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-80 kcal/mol
Surface area32890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.542, 181.354, 197.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-998-

HOH

21A-1003-

HOH

31B-57-

HOH

DetailsThe dimer in the asymmetric unit is the biological unit

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Components

#1: Protein 4-ALPHA-GLUCANOTRANSFERASE / Maltodextrin glycosyltransferase / amylomaltase / D-enzyme / Disproportionating enzyme / Oligo-1 / ...Maltodextrin glycosyltransferase / amylomaltase / D-enzyme / Disproportionating enzyme / Oligo-1 / 4-1 / 4-glucanotransferase


Mass: 51925.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: mgt / Plasmid: PTAM1 / Production host: Escherichia coli (E. coli) / Strain (production host): M5219 / References: UniProt: P80099, 4-alpha-glucanotransferase
#2: Sugar ChemComp-ACG / MODIFIED ACARBOSE PENTASACCHARIDE


Type: saccharide / Mass: 791.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C31H53NO22
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26-29% PEG 5000, 200-300 mM Ammonium Sulphate, 3 mM CaCl2, 80 mM MES, 40 mM acarbose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2001
RadiationMonochromator: Triangular single crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 39305 / % possible obs: 67 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.4 / Num. unique all: 979 / % possible all: 25

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LWH

1lwh


Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLF
RfactorNum. reflectionSelection details
Rfree0.302 -RANDOM
Rwork0.225 --
all-35705 -
obs-35705 -
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7312 0 110 41 7463
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5

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