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- PDB-1jib: Complex of Alpha-amylase II (TVA II) from Thermoactinomyces vulga... -

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Basic information

Entry
Database: PDB / ID: 1jib
TitleComplex of Alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with Maltotetraose Based on a Crystal Soaked with Maltohexaose.
ComponentsNEOPULLULANASE
KeywordsHYDROLASE / pullulan / cyclodextrin / neopullulanase / maltohexaose / maltotetraose
Function / homology
Function and homology information


neopullulanase activity / neopullulanase / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltotetraose / Neopullulanase 2
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsYokota, T. / Tonozuka, T. / Shimura, Y. / Ichikawa, K. / Kamitori, S. / Sakano, Y.
Citation
Journal: Biosci.Biotechnol.Biochem. / Year: 2001
Title: Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues.
Authors: Yokota, T. / Tonozuka, T. / Shimura, Y. / Ichikawa, K. / Kamitori, S. / Sakano, Y.
#1: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 2000
Title: Analysis of catalytic residues of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) by site-directed mutagenesis.
Authors: Ichikawa, K. / Tonozuka, T. / Yokota, T. / Shimura, Y. / Sakano, Y.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_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_atom_id / _atom_site.label_comp_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.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEOPULLULANASE
B: NEOPULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,4394
Polymers135,1062
Non-polymers1,3332
Water00
1
A: NEOPULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2202
Polymers67,5531
Non-polymers6671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEOPULLULANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2202
Polymers67,5531
Non-polymers6671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.870, 117.320, 112.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NEOPULLULANASE


Mass: 67553.125 Da / Num. of mol.: 2 / Mutation: D325N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Plasmid: pTND325N / Production host: Escherichia coli (E. coli) / Strain (production host): MV1184 / References: UniProt: Q08751, neopullulanase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, MES, CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 %(w/v)PEG60001reservoir
25 mM1reservoirCaCl2
340 mMMES1reservoirpH6.0
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→39.6 Å / Num. all: 107522 / Num. obs: 22140 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 17.765 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.137 / Net I/σ(I): 4.5
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.269 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 107522

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BVZ

1bvz


Resolution: 3.3→39.6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4478384.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.304 2182 10 %RANDOM
Rwork0.212 ---
all-22115 --
obs-21927 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.4191 Å2 / ksol: 0.284988 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-13.13 Å20 Å20 Å2
2---5.37 Å20 Å2
3----7.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3.3→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 90 0 9642
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 387 10.8 %
Rwork0.245 3184 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MTT_XPLOR.PARAMMTT_XPLOR.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 39.6 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_scbond_it1.542
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.361 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.245

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