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

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Basic information

Entry
Database: PDB / ID: 6iyg
TitleThe Structure of Maltooligosaccharide-forming Amylase from Pseudomonas saccharophila STB07 with Maltotetraose
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 region / 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-maltotetraose / Glucan 1,4-alpha-maltotetraohydrolase
Similarity search - Component
Biological speciesPelomonas saccharophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionDec 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)59,4325
Polymers58,6231
Non-polymers8094
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-18 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.280, 64.570, 168.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 58622.742 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-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M ammonium sulfate, 0.02 M Tris-HCl, 0.02 M maltotetraose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.5→42.436 Å / Num. obs: 80886 / % possible obs: 98.61 % / Redundancy: 6 % / CC1/2: 0.843 / Net I/σ(I): 2
Reflection shellResolution: 1.5→1.5177 Å / Num. unique obs: 1124 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWK

6iwk


Resolution: 1.5→42.436 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 4061 5.02 %
Rwork0.1674 76825 -
obs0.1683 80886 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.44 Å2 / Biso mean: 29.8288 Å2 / Biso min: 16.75 Å2
Refinement stepCycle: final / Resolution: 1.5→42.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 99 367 3727
Biso mean--50.89 36.85 -
Num. residues----415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.51770.31781410.2749254398
1.5177-1.53620.25121470.2581260098
1.5362-1.55560.24461500.2439258798
1.5556-1.57610.23551200.2453262398
1.5761-1.59770.2621340.2346261598
1.5977-1.62050.2481650.2296256998
1.6205-1.64470.22321420.205257098
1.6447-1.67040.2511400.1997260398
1.6704-1.69780.20291290.196262798
1.6978-1.72710.24551570.1898259898
1.7271-1.75850.21131270.1862262098
1.7585-1.79230.20211460.1816255896
1.7923-1.82890.20411100.1712263399
1.8289-1.86860.16651230.1749266299
1.8686-1.91210.18971210.17264599
1.9121-1.95990.18981290.1712266199
1.9599-2.01290.21191400.1741267599
2.0129-2.07210.19181410.1732262499
2.0721-2.1390.2211410.1665266499
2.139-2.21550.19291260.16322702100
2.2155-2.30420.18151520.16082655100
2.3042-2.4090.18491510.16652675100
2.409-2.5360.16581330.1624259897
2.536-2.69490.19871540.1612269299
2.6949-2.90290.18831630.16162700100
2.9029-3.1950.16841380.15832715100
3.195-3.65710.18591500.16432741100
3.6571-4.60660.1671610.14732784100
4.6066-42.4360.16131300.1674288698

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