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- PDB-1lwh: CRYSTAL STRUCTURE OF T. MARITIMA 4-ALPHA-GLUCANOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1lwh
TitleCRYSTAL STRUCTURE OF T. MARITIMA 4-ALPHA-GLUCANOTRANSFERASE
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / 4-alpha-glucanotransferase / alpha-amylase family / Thermotoga maritima / acarbose
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / alpha-amylase activity / oligosaccharide catabolic process / 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
4-alpha-glucanotransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 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 1.0Jul 3, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9324
Polymers103,8522
Non-polymers802
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-40 kcal/mol
Surface area34580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.567, 180.282, 199.222
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-989-

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: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 174 / 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 Å3/Da / Density % sol: 69.25 %
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, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Roujeinikova, A., (2001) Acta Crystallogr., Sect.D, 57, 1046.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
126-29 %(w/v)PEG5000 MME1reservoir
2200-300 mMammonium sulfate1reservoir
33 mM1reservoirCaCl2
480 mMMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 7, 2000
RadiationMonochromator: triangular single crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 45954 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2151 / % possible all: 63
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 100 Å / % possible obs: 89 % / Num. measured all: 247046 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 63 % / Rmerge(I) obs: 0.36

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2254 4.5 %RANDOM
Rwork0.224 ---
all-45037 --
obs-45037 89 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 2 174 7462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01

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