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- PDB-4s3q: Amylomaltase MalQ from Escherichia coli in complex with maltose -

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Basic information

Entry
Database: PDB / ID: 4s3q
TitleAmylomaltase MalQ from Escherichia coli in complex with maltose
Components4-alpha-glucanotransferase
KeywordsTRANSFERASE / Glucoside hydrolase clan H / maltose / maltodextrin / TIM barrel
Function / homology
Function and homology information


4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / beta-maltose 4-alpha-glucanotransferase activity / maltose catabolic 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
alpha-maltose / IODIDE ION / 4-alpha-glucanotransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

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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
C: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,61617
Polymers236,9483
Non-polymers1,66814
Water8,413467
1
A: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8307
Polymers78,9831
Non-polymers8476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4886
Polymers78,9831
Non-polymers5055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 4-alpha-glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2994
Polymers78,9831
Non-polymers3163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.132, 77.019, 128.403
Angle α, β, γ (deg.)76.110, 75.480, 66.310
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 78982.664 Da / Num. of mol.: 3
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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 %(w/v) PEG3350, 200 mM NaH2PO4, 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: 2.1→35 Å / Num. all: 138781 / Num. obs: 138781 / % possible obs: 94.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 36.54 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.015 / Net I/σ(I): 12.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.20.3943.034087118524196.4
2.2-2.40.2664.336227628228196.1
2.4-2.70.1556.86204228114195.9
2.7-30.08710.763934017858195.1
3-3.50.04617.393819517415193.1
3.5-40.0325.05206349462190.3
4-60.02628.862926213423189.6
6-80.02529.874573424193.6
8-100.0232.9726391215193.2
10-350.0233.3424301118181.7

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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: 2.1→34.23 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.2073 / FOM work R set: 0.7556 / SU B: 14.029 / SU ML: 0.182 / SU R Cruickshank DPI: 0.2463 / SU Rfree: 0.2013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 6970 5 %RANDOM
Rwork0.2208 ---
all0.2227 138780 --
obs0.2227 138780 94.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.6 Å2 / Biso mean: 39.119 Å2 / Biso min: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-1 Å2-0.05 Å2
2---0.88 Å20.15 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16350 0 51 467 16868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01916830
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215676
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.95122866
X-RAY DIFFRACTIONr_angle_other_deg0.769336054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75952043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11123.769804
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.025152763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.92615117
X-RAY DIFFRACTIONr_chiral_restr0.0720.22410
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02119122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023981
X-RAY DIFFRACTIONr_mcbond_it0.4360.998190
X-RAY DIFFRACTIONr_mcbond_other0.4360.998189
X-RAY DIFFRACTIONr_mcangle_it0.7711.48210227
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 516 -
Rwork0.294 9981 -
all-10497 -
obs--96.38 %
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)
13.34850.21372.54333.90921.84888.5011-0.00890.00320.07560.05670.06640.6424-0.1822-0.6681-0.05750.3898-0.00260.06490.33430.07540.3107-2.064-6.330521.0335
25.15224.18780.6215.1072.40542.39190.10440.0489-0.26110.2371-0.12080.05080.393-0.28280.01640.7956-0.1179-0.12370.14770.03110.475913.5365-36.476910.7914
31.30630.20790.46220.869-0.36281.9609-0.06380.1314-0.0274-0.08840.07280.01780.0070.0237-0.00910.5287-0.0121-0.00570.0813-0.05680.048627.133-3.15133.4859
40.49680.39830.18962.0926-0.17862.2433-0.0258-0.14210.04410.2218-0.0070.1249-0.20880.00620.03280.47950.0418-0.03680.1362-0.07790.0733.12334.290828.2465
57.9698-0.9541-0.42260.9967-0.9354.07060.1060.43480.4098-0.22610.01360.3149-0.201-0.2187-0.11970.47320.106-0.06010.4106-0.00690.2266-7.6342-32.1022-53.3075
65.30092.97440.04164.9639-0.43113.07430.01530.1143-0.0191-0.02020.07970.51810.2342-0.6822-0.0950.514-0.0704-0.01620.36180.02220.1687-10.5717-50.9579-23.7601
71.82950.0944-0.18110.61860.15260.70390.06550.0845-0.2263-0.0078-0.0564-0.03940.13-0.0128-0.00920.58790.0183-0.02850.1538-0.05190.043721.723-44.6919-40.2254
81.15080.1293-0.39681.4169-0.16231.49030.1685-0.03570.1190.0224-0.0790.0171-0.24970.0076-0.08950.56970.008-0.00040.1519-0.07160.046323.575-18.4559-35.6283
95.8015-3.0952-0.63156.0425-0.42765.3798-0.1251-0.1645-0.37350.29360.0060.6220.639-0.30070.11910.5982-0.07270.10950.1751-0.12790.4041-22.2371-51.085345.6055
106.59140.79422.57533.9303-0.79622.7788-0.00120.7475-0.2093-0.4549-0.01770.49620.1837-0.2030.01890.57890.0018-0.09190.5316-0.21190.2058-22.4612-33.687414.7902
111.2183-0.241-0.21791.45320.41860.8667-0.11620.0099-0.07820.08540.0380.16150.0387-0.02630.07830.45760.011-0.01290.1551-0.05270.0421-12.2278-17.962146.4323
120.7174-0.2755-0.11240.90240.19921.9367-0.1553-0.0767-0.12840.14550.1294-0.1570.2690.35980.02590.46880.0908-0.01090.2609-0.07550.106510.2633-31.375550.9331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 43
2X-RAY DIFFRACTION2A52 - 129
3X-RAY DIFFRACTION3A130 - 485
4X-RAY DIFFRACTION4A486 - 691
5X-RAY DIFFRACTION5B2 - 43
6X-RAY DIFFRACTION6B52 - 129
7X-RAY DIFFRACTION7B130 - 485
8X-RAY DIFFRACTION8B486 - 694
9X-RAY DIFFRACTION9C2 - 43
10X-RAY DIFFRACTION10C52 - 129
11X-RAY DIFFRACTION11C130 - 485
12X-RAY DIFFRACTION12C486 - 690

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