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- PDB-6jqb: The structure of maltooligosaccharide-forming amylase from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 6jqb
TitleThe structure of maltooligosaccharide-forming amylase from Pseudomonas saccharophila STB07 with pseudo-maltoheptaose
ComponentsGlucan 1,4-alpha-maltotetraohydrolase
KeywordsHYDROLASE / Maltooligosaccharide-forming amylase / saccharophila STB07 / Sugar binding protein
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
ACARBOSE DERIVED HEPTASACCHARIDE / Glucan 1,4-alpha-maltotetraohydrolase
Similarity search - Component
Biological speciesPelomonas saccharophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.101 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 China (NSFC)31722040 China
National Natural Science Foundation of China (NSFC)31571882 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structure of maltotetraose-forming amylase from Pseudomonas saccharophila STB07 provides insights into its product specificity.
Authors: Zhang, Z. / Jin, T. / Xie, X. / Ban, X. / Li, C. / Hong, Y. / Cheng, L. / Gu, Z. / Li, Z.
History
DepositionMar 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 2.0Apr 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / entity / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.number_obs / _reflns_shell.number_unique_obs / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Chirality error / Details: incorrect chiral volumes resolved. / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _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)59,1096
Polymers57,7941
Non-polymers1,3155
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.900, 63.735, 163.727
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: 57793.852 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-7SA / ACARBOSE DERIVED HEPTASACCHARIDE / (2R,3R,4R,5S,6R)-6-(hydroxymethyl)-5-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-5-[(2R,3R,4S,5S,6R)-5-[[(1S,4R,5R,6S)-3-(hydroxymethyl)-4-[(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-5-[(2R,3R,4S,5S,6R)-5-[[(1S,4R,5S,6S)-3-(hydroxymethyl)-4,5,6-tris(oxidanyl)cyclohex-2-en-1-yl]amino]-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-5,6-bis(oxidanyl)cyclohex-2-en-1-yl]amino]-6-methyl-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-oxane-2,3,4-triol


Type: saccharideCarbohydrate / Mass: 1111.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C44H74N2O30
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M ammonium sulfate, 0.2 M Tris-HCl, 20 mM acarbose, 20 mM maltoheptaose

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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: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 211320 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/av σ(I): 45.159 / Net I/σ(I): 1.36
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 5.432 / Num. unique obs: 10184 / Rsym value: 0.508 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWK

6iwk


Resolution: 1.101→38.292 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1707 10184 5.03 %
Rwork0.1561 192271 -
obs0.1568 202455 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.47 Å2 / Biso mean: 13.51 Å2 / Biso min: 6.8 Å2
Refinement stepCycle: final / Resolution: 1.101→38.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 170 393 3826
Biso mean--16.72 22.36 -
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 (%)
1.101-1.1130.193580.1642615197
1.113-1.12610.18583470.1545629399
1.1261-1.13980.1763630.1499636899
1.1398-1.15430.16693460.1521624299
1.1543-1.16950.17593420.143634599
1.1695-1.18550.16883410.1441630599
1.1855-1.20240.15753480.14146380100
1.2024-1.22040.16353090.13726338100
1.2204-1.23940.15323330.14226362100
1.2394-1.25980.16513110.13786398100
1.2598-1.28150.16533450.14616375100
1.2815-1.30480.17843240.1498638099
1.3048-1.32990.17673080.14946426100
1.3299-1.3570.17793510.15156340100
1.357-1.38650.17993180.156390100
1.3865-1.41880.16133300.15246440100
1.4188-1.45430.16183350.15056407100
1.4543-1.49360.16723810.15136356100
1.4936-1.53750.16643120.1516410100
1.5375-1.58720.183560.14736403100
1.5872-1.64390.17413330.15566435100
1.6439-1.70970.17663550.15446403100
1.7097-1.78750.17483480.15926423100
1.7875-1.88180.18653230.16246477100
1.8818-1.99970.1713530.15646477100
1.9997-2.1540.16053410.15566461100
2.154-2.37080.17573520.15036500100
2.3708-2.71380.16083370.15596545100
2.7138-3.41870.17313260.1676633100
3.4187-6.80.16993580.166680899

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