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- PDB-4s3p: Amylomaltase MalQ from Escherichia coli, apo structure -

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Basic information

Entry
Database: PDB / ID: 4s3p
TitleAmylomaltase MalQ from Escherichia coli, apo structure
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / 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
4-alpha-glucanotransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.4Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)157,9652
Polymers157,9652
Non-polymers00
Water3,369187
1
A: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)78,9831
Polymers78,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)78,9831
Polymers78,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-23 kcal/mol
Surface area57480 Å2
MethodPISA
4
A: 4-alpha-glucanotransferase

A: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)157,9652
Polymers157,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2560 Å2
ΔGint-12 kcal/mol
Surface area58600 Å2
MethodPISA
5
B: 4-alpha-glucanotransferase

B: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)157,9652
Polymers157,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2040 Å2
ΔGint-10 kcal/mol
Surface area60020 Å2
MethodPISA
6
A: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase

A: 4-alpha-glucanotransferase
B: 4-alpha-glucanotransferase


Theoretical massNumber of molelcules
Total (without water)315,9314
Polymers315,9314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area13800 Å2
ΔGint-64 kcal/mol
Surface area109420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.337, 106.811, 217.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein 4-alpha-glucanotransferase / Amylomaltase / Disproportionating enzyme / D-enzyme


Mass: 78982.664 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.2 M Na3Citrate, 250 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: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013 / Details: mirror
RadiationMonochromator: Si 111 DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→35 Å / Num. all: 49608 / Num. obs: 49608 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 38.186 Å2 / Rmerge(I) obs: 0.131 / Χ2: 0.927 / Net I/σ(I): 13.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.8-2.90.6722.82257364885199.9
2.9-30.5433.51225104279199.9
3-3.20.3844.91370687051199.9
3.2-3.50.2118.55408177761199.8
3.5-40.11514.55438848361199.6
4-60.07321.66267412043199.3
6-80.06522.97152512985198.9
8-100.03139.2354581087198.5
10-350.02541.5153181156193.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S3R

4s3r


Resolution: 2.8→33.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.1819 / WRfactor Rwork: 0.1457 / FOM work R set: 0.8312 / SU B: 26.506 / SU ML: 0.239 / SU R Cruickshank DPI: 1.0898 / SU Rfree: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.09 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 2410 4.9 %RANDOM
Rwork0.1797 ---
all0.1819 49608 --
obs0.1819 49608 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.03 Å2 / Biso mean: 41.916 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.43 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10994 0 0 187 11181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911287
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210541
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9515343
X-RAY DIFFRACTIONr_angle_other_deg0.718324239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46551378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.723.738535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.526151864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2891580
X-RAY DIFFRACTIONr_chiral_restr0.0590.21622
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02112852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022666
X-RAY DIFFRACTIONr_mcbond_it0.6772.2165517
X-RAY DIFFRACTIONr_mcbond_other0.6772.2165516
X-RAY DIFFRACTIONr_mcangle_it1.1993.3226894
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 194 -
Rwork0.294 3412 -
all-3606 -
obs--99.92 %
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)
17.18011.25482.89141.97630.54374.147-0.0475-0.6343-0.26020.355-0.14840.03550.1121-0.03010.19590.08080.0120.03180.20440.06360.046121.8708105.574763.4743
25.09871.6513.10314.90110.96667.14290.0287-0.52560.36670.5678-0.064-0.1944-0.26230.02850.03520.2530.0099-0.02190.0869-0.07920.148729.2119136.768359.0491
31.61380.14370.0230.55590.15441.4357-0.03790.0990.0323-0.11970.00220.1068-0.0975-0.0930.03570.08270.0161-0.03520.03260.00290.024919.448111.831829.85
46.17931.6461-1.50625.7467-2.31564.90550.0442-0.52060.12690.4379-0.3466-0.7946-0.03760.51810.30230.23050.0935-0.03250.3049-0.06270.32862.666981.74142.4335
53.02361.1182.36234.4918-0.87278.8645-0.0089-0.3319-0.03830.2611-0.0489-0.29270.13850.33690.05780.34780.1188-0.06380.12850.01230.218454.376551.148245.8623
61.1651-0.48520.2020.8895-0.29681.7120.0598-0.0407-0.1865-0.04830.03120.11280.24210.0125-0.0910.25280.049-0.02170.03540.01210.104836.536276.094320.8203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 52
2X-RAY DIFFRACTION2A53 - 129
3X-RAY DIFFRACTION3A130 - 691
4X-RAY DIFFRACTION4B2 - 52
5X-RAY DIFFRACTION5B53 - 129
6X-RAY DIFFRACTION6B130 - 690

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