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- PDB-1obb: alpha-glucosidase A, AglA, from Thermotoga maritima in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1obb
Titlealpha-glucosidase A, AglA, from Thermotoga maritima in complex with maltose and NAD+
ComponentsALPHA-GLUCOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE / SULFINIC ACID / NAD+ / MALTOSE
Function / homology
Function and homology information


alpha-glucosidase / : / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / metal ion binding
Similarity search - Function
LDH C-terminal domain-like / AglA-like glucosidase / Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily ...LDH C-terminal domain-like / AglA-like glucosidase / Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-glucosidase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsLodge, J.A. / Maier, T. / Liebl, W. / Hoffmann, V. / Strater, N.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Thermotoga Maritima Alpha-Glucosidase Agla Defines a New Clan of Nad+-Dependent Glycosidases
Authors: Lodge, J.A. / Maier, T. / Liebl, W. / Hoffmann, V. / Strater, N.
History
DepositionJan 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 10, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-GLUCOSIDASE
B: ALPHA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3206
Polymers110,3082
Non-polymers2,0114
Water11,638646
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.000, 85.700, 83.600
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98427, 0.17666, 0.00361), (0.17667, 0.98365, 0.03484), (0.00261, 0.03493, -0.99939)
Vector: 29.66571, -2.46927, -1.60929)

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Components

#1: Protein ALPHA-GLUCOSIDASE / MALTASE


Mass: 55154.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Plasmid: PUN121 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DSM 3109 / Variant (production host): JM83 / References: UniProt: O33830, alpha-glucosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.586 Å3/Da / Density % sol: 50.6 %
Crystal growpH: 5
Details: 10% PEG 6000, 1M LICL, 0.1M TRIS/HCL PH4.6, 2MM MNCL2, 50MM MALTOSE, 50MM NAD+, pH 5.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMTris1droppH7.0
310 %(w/v)PEG60001reservoir
41 M1reservoirLiCl
5100 mMTris-HCl1reservoirpH4.6
62 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5475
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2001 / Details: OSMIC MULTILAYER MAX-FLUX
RadiationMonochromator: OSMIC MULTILAYER MAX-FLUX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5475 Å / Relative weight: 1
ReflectionResolution: 1.9→24 Å / Num. obs: 77496 / % possible obs: 98.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.4 / % possible all: 93.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / % possible obs: 96.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Lowest resolution: 1.97 Å / % possible obs: 92.6 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→17.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1732125.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2347 3 %RANDOM
Rwork0.199 ---
obs0.199 77467 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.5501 Å2 / ksol: 0.378793 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-2.62 Å2
2--7.89 Å20 Å2
3----7.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→17.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7721 0 134 646 8501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 369 3 %
Rwork0.294 11922 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_CSW.PARAPROTEIN.TOP
X-RAY DIFFRACTION2MAL.PARAMMAL.TOPO
X-RAY DIFFRACTION3NAD.PARAMNAD.TOPO
X-RAY DIFFRACTION4CIS_PEPTIDE.PARA
X-RAY DIFFRACTION5WATER_REP.PARAM
Refinement
*PLUS
Rfactor Rfree: 0.234 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Lowest resolution: 1.97 Å

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