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- PDB-1k1x: Crystal structure of 4-alpha-glucanotransferase from thermococcus... -

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Basic information

Entry
Database: PDB / ID: 1k1x
TitleCrystal structure of 4-alpha-glucanotransferase from thermococcus litoralis
Components4-ALPHA-GLUCANOTRANSFERASE
KeywordsTRANSFERASE / 4-ALPHA-GLUCANOTRANSFERASE
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
7-stranded beta/alpha barrel - #20 / Alpha-amylase/4-alpha-glucanotransferase, central domain / Alpha-amylase/4-alpha-glucanotransferase, C-terminal / Alpha-amylase/4-alpha-glucanotransferase, middle domain / Alpha-amylase/4-alpha-glucanotransferase, C-terminal / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / 7-stranded beta/alpha barrel / Glycoside hydrolase families 57/38, central domain superfamily / Beta-galactosidase; Chain A, domain 5 - #10 ...7-stranded beta/alpha barrel - #20 / Alpha-amylase/4-alpha-glucanotransferase, central domain / Alpha-amylase/4-alpha-glucanotransferase, C-terminal / Alpha-amylase/4-alpha-glucanotransferase, middle domain / Alpha-amylase/4-alpha-glucanotransferase, C-terminal / Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / 7-stranded beta/alpha barrel / Glycoside hydrolase families 57/38, central domain superfamily / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-alpha-glucanotransferase
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsImamura, H. / Fushinobu, S. / Kumasaka, T. / Yamamoto, M. / Jeon, B.S. / Wakagi, T. / Matsuzawa, H.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor
Authors: Imamura, H. / Fushinobu, S. / Yamamoto, M. / Kumasaka, T. / Jeon, B.S. / Wakagi, T. / Matsuzawa, H.
History
DepositionSep 26, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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)156,2216
Polymers155,9782
Non-polymers2424
Water8,989499
1
A: 4-ALPHA-GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0292
Polymers77,9891
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-ALPHA-GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1914
Polymers77,9891
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-26 kcal/mol
Surface area46000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)137.682, 161.494, 70.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 4-ALPHA-GLUCANOTRANSFERASE /


Mass: 77989.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (archaea) / Plasmid: pUT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32462, 4-alpha-glucanotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD, CALCIUM CHLORIDE, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
135 %(w/v)MPD1reservoir
220 mM1reservoirCaCl2
30.1 MTris-HCl1reservoirpH8.0
410-20 mg/mlprotein1drop
55 mMTris-HCl1droppH7.5
610 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 394421 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.157 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 61753 / % possible obs: 99.9 % / Num. measured all: 274277 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Lowest resolution: 2.53 Å / % possible obs: 99.9 % / Num. unique obs: 8891 / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2829762.54 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3101 5 %RANDOM
Rwork0.195 ---
all0.197 62208 --
obs0.197 62015 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.3653 Å2 / ksol: 0.308002 e/Å3
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2---0.47 Å20 Å2
3---1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10695 0 11 499 11205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
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
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 517 5.1 %
Rwork0.232 9639 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.334 / Rfactor Rwork: 0.255

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