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- PDB-3a6o: Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylas... -

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Basic information

Entry
Database: PDB / ID: 3a6o
TitleCrystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase 2/acarbose complex
ComponentsNeopullulanase 2
KeywordsHYDROLASE / Acarbose / amylase / complex / Calcium / Carbohydrate metabolism / Glycosidase / Metal-binding
Function / homology
Function and homology information


neopullulanase / neopullulanase activity / 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 / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACARBOSE DERIVED PENTASACCHARIDE / Neopullulanase 2
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOhtaki, A. / Mizuno, M. / Tonozuka, T. / Sakano, Y. / Kamitori, S.
CitationJournal: J.BIOL.CHEM. / Year: 2004
Title: Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism
Authors: Ohtaki, A. / Mizuno, M. / Tonozuka, T. / Sakano, Y. / Kamitori, S.
History
DepositionSep 7, 2009Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 22, 2009ID: 1VFK
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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

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Assembly

Deposited unit
A: Neopullulanase 2
B: Neopullulanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8046
Polymers135,1082
Non-polymers1,6964
Water7,314406
1
A: Neopullulanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4023
Polymers67,5541
Non-polymers8482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neopullulanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4023
Polymers67,5541
Non-polymers8482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.599, 119.258, 113.007
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 2 / / Alpha-amylase II / TVA II


Mass: 67554.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Strain: R-47 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08751, neopullulanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-ARE / ACARBOSE DERIVED PENTASACCHARIDE / 4-O-(4,6-DIDEOXY-4-{[4-[(4-O-HEXOPYRANOSYLHEXOPYRANOSYL)OXY]-5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}HE XOPYRANOSYL)HEXOPYRANOSE


Type: saccharideCarbohydrate / Mass: 807.745 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C31H53NO23
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→38.81 Å / Num. all: 35055 / Num. obs: 35055 / Biso Wilson estimate: 70.6 Å2 / Rmerge(I) obs: 0.084
Reflection shellHighest resolution: 2.8 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.2.0005refinement
PROCESSdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→38.81 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.751 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23106 3455 9 %RANDOM
Rwork0.15706 ---
obs0.16402 35055 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.796 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2---0.9 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9550 0 112 406 10068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0229928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4931.9613458
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13951168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74123.042526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5441590
X-RAY DIFFRACTIONr_chiral_restr0.1530.21414
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.25211
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3380.26644
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2644
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3030.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2981.55982
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.19829320
X-RAY DIFFRACTIONr_scbond_it3.30434576
X-RAY DIFFRACTIONr_scangle_it5.1114.54138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.246 2766 -
Rfree-0 -
obs--100 %

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