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- PDB-4s3r: Amylomaltase MalQ from Escherichia coli in complex with the pseud... -

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Basic information

Entry
Database: PDB / ID: 4s3r
TitleAmylomaltase MalQ from Escherichia coli in complex with the pseudo-heptasaccharide acarviosine-glucose-acarbose
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / Acarbose-derived heptasaccharide / glucoside hydrolase clan H / maltose / maltodextrin / TIM barrel
Function / homology
Function and homology information


maltose catabolic process / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / glycogen biosynthetic process / glycogen catabolic process / cytosol
Similarity search - Function
: / MalQ N-terminal beta sandwich domain / Glycoside hydrolase, family 77 / 4-alpha-glucanotransferase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACARBOSE DERIVED HEPTASACCHARIDE / 4-alpha-glucanotransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWeiss, S.C. / Schiefner, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli.
Authors: Weiss, S.C. / Skerra, A. / Schiefner, A.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1873
Polymers80,0141
Non-polymers1,1732
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 75.830, 163.850
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 / D-enzyme


Mass: 80014.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: b3416, JW3379, malA, malQ / Plasmid: pASK75-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P15977, 4-alpha-glucanotransferase
#2: 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: saccharide / Mass: 1111.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C44H74N2O30
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE DEPOSITORS STATE THAT THE FREE ANOMERIC C1 OF THE TERMINAL GLUCOSE MOIETY ADOPTS BOTH ALPHA-D ...THE DEPOSITORS STATE THAT THE FREE ANOMERIC C1 OF THE TERMINAL GLUCOSE MOIETY ADOPTS BOTH ALPHA-D GLUCOSE AND BETA-D-GLUCOSE CONFIGURATIONS, OF WHICH THE BETA OCCURS IN 64 % OF THE MOLECULES. THE BETA-FORM WAS BUILT BECAUSE IT BETTER FITS THE ELECTRON DENSITY.

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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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12 %(w/v) PEG3350, 350 mM NaCl, 20 mM Tris-HCl, protein concentration 13 mg/ml, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98206, 0.98004, 0.97982, 0.97857
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: mirror
RadiationMonochromator: Si 111 DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.982061
20.980041
30.979821
40.978571
ReflectionNumber: 353886 / Rmerge(I) obs: 0.073 / Χ2: 1 / D res high: 2.1 Å / Num. obs: 91105 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
105083110.025
610305710.03
46925510.038
3.54651410.044
33.51153210.06
2.731159010.103
2.52.71115810.165
2.42.5704710.223
2.32.4833410.282
2.22.3992910.378
2.12.21185810.541
ReflectionResolution: 2.1→50 Å / Num. all: 48101 / Num. obs: 48101 / % possible obs: 99.98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 38.93 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.99 / Net I/σ(I): 17.19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.20.5843.534600261531100
2.2-2.30.4075.013846551541100
2.3-2.50.2717.255997680201100
2.5-2.70.17810.664359658361100
2.7-30.11115.834530760921100
3-3.50.06425.084485961081100
3.5-40.04734.962505634821100
4-60.04139.043559750171100
6-100.03240.92119761722199.9
10-500.02641.253145517198.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MAR345data collection
XDSdata reduction
HKL2Mapphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→47.25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1928 / WRfactor Rwork: 0.1603 / FOM work R set: 0.8504 / SU B: 9.326 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1813 / SU Rfree: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 2433 5.1 %RANDOM
Rwork0.1691 ---
all0.1709 48101 --
obs0.1709 48101 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.72 Å2 / Biso mean: 39.181 Å2 / Biso min: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å20 Å2
2---1.32 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5421 0 80 226 5727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195651
X-RAY DIFFRACTIONr_bond_other_d0.0010.025246
X-RAY DIFFRACTIONr_angle_refined_deg1.41.987690
X-RAY DIFFRACTIONr_angle_other_deg0.933312084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5085678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18923.774265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0215854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8411539
X-RAY DIFFRACTIONr_chiral_restr0.0780.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
X-RAY DIFFRACTIONr_mcbond_it1.2032.4542718
X-RAY DIFFRACTIONr_mcbond_other1.2032.4532717
X-RAY DIFFRACTIONr_mcangle_it1.853.6733394
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 168 -
Rwork0.243 3322 -
all-3490 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.69642.5431.62092.77981.30337.0034-0.10920.05430.0755-0.0797-0.01920.42680.0946-0.59240.12840.1202-0.05740.03980.2655-0.02890.3805-8.36081.291519.6744
23.33112.4944-0.17866.37530.6211.2597-0.010.1054-0.09830.0502-0.030.1880.058-0.13720.040.23920.01250.03290.0550.0350.191711.8611-27.620227.3253
31.27470.3276-0.18490.8137-0.1361.3136-0.05480.16-0.1778-0.0309-0.0032-0.020.22760.06590.05790.08090.010.00520.0283-0.02180.028224.98223.946512.6042
40.5244-0.0586-0.0291.27550.23481.4233-0.0001-0.16910.05960.2888-0.02810.08880.00010.02770.02820.1117-0.02310.00520.0597-0.01830.019918.917519.433233.3421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 42
2X-RAY DIFFRACTION2A52 - 129
3X-RAY DIFFRACTION3A130 - 485
4X-RAY DIFFRACTION4A486 - 690

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