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- PDB-1ug9: Crystal Structure of Glucodextranase from Arthrobacter globiformis I42 -

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Basic information

Entry
Database: PDB / ID: 1ug9
TitleCrystal Structure of Glucodextranase from Arthrobacter globiformis I42
Componentsglucodextranase
KeywordsHYDROLASE / alpha-alpha-six-barrels / GH Family 15
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase activity / glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glucodextranase, domain B / Glucodextranase-like, C-terminal / C-terminal binding-module, SLH-like, of glucodextranase / Glucoamylase, bacterial / Glucodextranase, N-terminal / Glucodextranase, domain N / Immunoglobulin-like - #1190 / : / Glucoamylase active site region signature. / GH15-like domain ...Glucodextranase, domain B / Glucodextranase-like, C-terminal / C-terminal binding-module, SLH-like, of glucodextranase / Glucoamylase, bacterial / Glucodextranase, N-terminal / Glucodextranase, domain N / Immunoglobulin-like - #1190 / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Beta-galactosidase; Chain A, domain 5 - #10 / Glycosyltransferase - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMizuno, M. / Tonozuka, T. / Suzuki, S. / Uotsu-Tomita, R. / Ohtaki, A. / Kamitori, S. / Nishikawa, A. / Sakano, Y.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural insights into substrate specificity and function of glucodextranase
Authors: Mizuno, M. / Tonozuka, T. / Suzuki, S. / Uotsu-Tomita, R. / Kamitori, S. / Nishikawa, A. / Sakano, Y.
History
DepositionJun 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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: glucodextranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8598
Polymers106,5271
Non-polymers3337
Water9,926551
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.860, 88.535, 80.781
Angle α, β, γ (deg.)90.00, 113.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein glucodextranase


Mass: 106526.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arthrobacter globiformis (bacteria) / Strain: I42 / References: UniProt: Q9LBQ9, glucan 1,6-alpha-glucosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.91 Å3/Da / Density % sol: 57.4 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
220 mMsodium acetate1droppH6.0
35 mMcalcium acetate1drop
43.0 %(w/v)PEG80001reservoir
580 mMpotassium dihydrogen phosphate1reservoir
650 mMsodium acetate1reservoirpH5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→19.881 Å / Num. all: 45620 / Num. obs: 45620 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.216 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 50 Å / Num. obs: 48376 / % possible obs: 96 % / Num. measured all: 193427 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 2.51 Å / % possible obs: 62.1 % / Rmerge(I) obs: 0.223

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LF6

1lf6


Resolution: 2.5→19.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4085992.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4522 10.1 %RANDOM
Rwork0.189 ---
obs0.19 44858 99.8 %-
all-45620 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0677 Å2 / ksol: 0.321673 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å27.74 Å2
2---5.81 Å20 Å2
3---1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 12 551 8069
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 710 9.6 %
Rwork0.219 6698 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5GOL.PARAMGOL.TOP
Refinement
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 19.9 Å / Num. reflection obs: 48379 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Highest resolution: 2.42 Å / Lowest resolution: 2.51 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.254

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