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- PDB-6m6t: Amylomaltase from Streptococcus agalactiae in complex with acarbose -

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Basic information

Entry
Database: PDB / ID: 6m6t
TitleAmylomaltase from Streptococcus agalactiae in complex with acarbose
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / amylomaltase / 4-alpha-glucanotransferase / cyclodextrin / acarbose
Function / homologyGlycoside hydrolase, family 77 / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / Glycoside hydrolase superfamily / alpha-acarbose / acarbose-derived trisaccharide / 4-alpha-glucanotransferase
Function and homology information
Biological speciesStreptococcus agalactiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsWangkanont, K. / Tumhom, S. / Pongsawasdi, P.
CitationJournal: Sci Rep / Year: 2021
Title: Streptococcus agalactiae amylomaltase offers insight into the transglycosylation mechanism and the molecular basis of thermostability among amylomaltases.
Authors: Tumhom, S. / Nimpiboon, P. / Wangkanont, K. / Pongsawasdi, P.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase
C: 4-alpha-glucanotransferase
D: 4-alpha-glucanotransferase
E: 4-alpha-glucanotransferase
F: 4-alpha-glucanotransferase
G: 4-alpha-glucanotransferase
H: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,98224
Polymers471,8728
Non-polymers8,11016
Water4,540252
1
A: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9353
Polymers58,9841
Non-polymers9512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint2 kcal/mol
Surface area21430 Å2
MethodPISA
2
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9353
Polymers58,9841
Non-polymers9512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint3 kcal/mol
Surface area21410 Å2
MethodPISA
3
C: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0973
Polymers58,9841
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint3 kcal/mol
Surface area21850 Å2
MethodPISA
4
D: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9353
Polymers58,9841
Non-polymers9512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint3 kcal/mol
Surface area21680 Å2
MethodPISA
5
E: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0973
Polymers58,9841
Non-polymers1,1132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint3 kcal/mol
Surface area21920 Å2
MethodPISA
6
F: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9353
Polymers58,9841
Non-polymers9512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint3 kcal/mol
Surface area21510 Å2
MethodPISA
7
G: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1133
Polymers58,9841
Non-polymers1,1292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area21210 Å2
MethodPISA
8
H: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9353
Polymers58,9841
Non-polymers9512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint3 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.748, 216.072, 224.503
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
4-alpha-glucanotransferase / / Amylomaltase / Disproportionating enzyme


Mass: 58983.957 Da / Num. of mol.: 8 / Fragment: amylomaltase, UNP residues 2-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: malQ / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: A0A0E1EIJ0, 4-alpha-glucanotransferase
#2: Polysaccharide
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-1,5-anhydro-D-glucitol


Type: oligosaccharide / Mass: 467.465 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[h2122h_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#3: Polysaccharide
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / acarbose-derived trisaccharide


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 483.465 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: acarbose-derived trisaccharide
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#4: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.87 % / Mosaicity: 0.19 °
Crystal growTemperature: 289 K / Method: batch mode / pH: 7.5
Details: 100 mM Tris, 100 mM Magnesium Formate, 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 2.75→29.822 Å / Num. obs: 129800 / % possible obs: 98.9 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.055 / Rrim(I) all: 0.147 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.75-2.85.90.843736563170.7450.3770.9242.198.1
15.06-29.825.70.06643717610.9950.030.07321.584

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.75 Å29.82 Å
Translation2.75 Å29.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TZ7

1tz7


Resolution: 2.75→29.82 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.59
RfactorNum. reflection% reflection
Rfree0.2869 6483 5 %
Rwork0.2054 --
obs0.2095 129572 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.22 Å2 / Biso mean: 50.6582 Å2 / Biso min: 19.45 Å2
Refinement stepCycle: final / Resolution: 2.75→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32579 0 554 252 33385
Biso mean--61.37 43.17 -
Num. residues----3974
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.84820.38526050.28651212598
2.8482-2.96220.39166790.27491213498
2.9622-3.09680.35256360.25251216299
3.0968-3.25990.33666010.24451226699
3.2599-3.46390.32336140.23651228799
3.4639-3.73090.29587230.21991217999
3.7309-4.10550.3176540.20211229999
4.1055-4.69750.24646280.17781241999
4.6975-5.91080.2466770.17081242499
5.9108-29.820.21516660.16481279498

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