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- PDB-6j3x: The Structure of Maltooligosaccharide-forming Amylase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 6j3x
TitleThe Structure of Maltooligosaccharide-forming Amylase from Pseudomonas saccharophila STB07 with Maltotriose
ComponentsGlucan 1,4-alpha-maltotetraohydrolase
KeywordsSUGAR BINDING PROTEIN / Maltooligosaccharide-forming Amylase / Pseudomonas saccharophila STB07
Function / homology
Function and homology information


glucan 1,4-alpha-maltotetraohydrolase / glucan 1,4-alpha-maltotetraohydrolase activity / starch catabolic process / starch binding / alpha-amylase activity / extracellular space / metal ion binding
Similarity search - Function
Glucan 1,4-alpha-maltotetraohydrolase, domain C / Glucan 1,4-alpha-maltotetraohydrolase, domain C / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain ...Glucan 1,4-alpha-maltotetraohydrolase, domain C / Glucan 1,4-alpha-maltotetraohydrolase, domain C / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltotriose / Glucan 1,4-alpha-maltotetraohydrolase
Similarity search - Component
Biological speciesPelomonas saccharophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLi, Z.F. / Ban, X.F. / Zhang, Z.Q. / Li, C.M. / Gu, Z.B. / Jin, T.C. / Li, Y.L. / Shang, Y.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31722040 China
National Natural Science Foundation of China31571882 China
CitationJournal: To Be Published
Title: Maltotetraose-forming amylase from Pseudomonas saccharophila STB07
Authors: Zhang, Z.Q. / Ban, X.F. / Li, Z.F. / Jin, T.C. / Li, Y.L. / Gu, Z.B. / Li, C.M. / Shang, Y.H.
History
DepositionJan 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucan 1,4-alpha-maltotetraohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5166
Polymers57,8071
Non-polymers7095
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.320, 64.650, 169.010
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 Glucan 1,4-alpha-maltotetraohydrolase / G4-amylase / Exo-maltotetraohydrolase / Maltotetraose-forming amylase / Maltotetraose-forming exo-amylase


Mass: 57806.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelomonas saccharophila (bacteria) / Gene: mta / Production host: Bacillus subtilis (bacteria)
References: UniProt: P22963, glucan 1,4-alpha-maltotetraohydrolase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M ammonium sulfate, 0.02 M Tris-NCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.62→42.47 Å / Num. obs: 65292 / % possible obs: 99.61 % / Redundancy: 6 % / Net I/σ(I): 1.38
Reflection shellResolution: 1.62→4.67 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWK

6iwk


Resolution: 1.62→42.47 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.71
RfactorNum. reflection% reflection
Rfree0.1861 3329 5.1 %
Rwork0.1637 --
obs0.1649 65292 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 44 307 3615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013411
X-RAY DIFFRACTIONf_angle_d1.134642
X-RAY DIFFRACTIONf_dihedral_angle_d3.3091903
X-RAY DIFFRACTIONf_chiral_restr0.06455
X-RAY DIFFRACTIONf_plane_restr0.007615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.64310.25921420.23182537X-RAY DIFFRACTION100
1.6431-1.66770.26161490.22892544X-RAY DIFFRACTION100
1.6677-1.69370.28131380.21572555X-RAY DIFFRACTION100
1.6937-1.72150.23631340.20322538X-RAY DIFFRACTION99
1.7215-1.75120.21651400.20092519X-RAY DIFFRACTION99
1.7512-1.7830.19831210.18592596X-RAY DIFFRACTION100
1.783-1.81730.21261310.19072503X-RAY DIFFRACTION99
1.8173-1.85440.22261510.17752574X-RAY DIFFRACTION99
1.8544-1.89470.23341410.1782521X-RAY DIFFRACTION100
1.8947-1.93880.20341250.16442587X-RAY DIFFRACTION100
1.9388-1.98730.18451330.17132552X-RAY DIFFRACTION99
1.9873-2.0410.2011330.16242562X-RAY DIFFRACTION100
2.041-2.10110.20351300.16142582X-RAY DIFFRACTION100
2.1011-2.16890.17111400.15792562X-RAY DIFFRACTION100
2.1689-2.24640.18141270.15732576X-RAY DIFFRACTION100
2.2464-2.33640.15971450.15822600X-RAY DIFFRACTION100
2.3364-2.44270.20631270.16352589X-RAY DIFFRACTION100
2.4427-2.57150.20531430.15942574X-RAY DIFFRACTION99
2.5715-2.73250.21061520.1622598X-RAY DIFFRACTION100
2.7325-2.94350.19641360.16622602X-RAY DIFFRACTION100
2.9435-3.23960.19641460.16072596X-RAY DIFFRACTION100
3.2396-3.70810.16021460.16272628X-RAY DIFFRACTION100
3.7081-4.67090.16551430.14432681X-RAY DIFFRACTION99
4.6709-42.48770.1711560.16992787X-RAY DIFFRACTION99

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