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- PDB-6ag8: Crystal structure of Maltose O-acetyltransferase from E. coli -

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Basic information

Entry
Database: PDB / ID: 6ag8
TitleCrystal structure of Maltose O-acetyltransferase from E. coli
ComponentsMaltose O-acetyltransferase
KeywordsTRANSFERASE / maltose O-acetyltransferase
Function / homology
Function and homology information


maltose O-acetyltransferase / maltose O-acetyltransferase activity / O-acyltransferase activity / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
: / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...: / Maltose/galactoside acetyltransferase / Maltose acetyltransferase hexapeptide capping motif / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Maltose O-acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsJoo, S. / Kim, K.-J.
CitationJournal: To Be Published
Title: Metabolic engineering of Escherichia coli for production of non-natural acetins from glycerol
Authors: Zada, B. / Joo, S. / Wang, C. / Kim, K.-J. / Kim, S.-W.
History
DepositionAug 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
C: Maltose O-acetyltransferase
A: Maltose O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6254
Polymers42,3802
Non-polymers2442
Water5,350297
1
C: Maltose O-acetyltransferase
hetero molecules

C: Maltose O-acetyltransferase
hetero molecules

C: Maltose O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9376
Polymers63,5703
Non-polymers3663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7810 Å2
ΔGint-10 kcal/mol
Surface area20340 Å2
MethodPISA
2
A: Maltose O-acetyltransferase
hetero molecules

A: Maltose O-acetyltransferase
hetero molecules

A: Maltose O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9376
Polymers63,5703
Non-polymers3663
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7840 Å2
ΔGint-13 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.104, 62.104, 81.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11C-413-

HOH

21C-422-

HOH

31C-429-

HOH

41A-414-

HOH

51A-422-

HOH

61A-441-

HOH

71A-447-

HOH

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Components

#1: Protein Maltose O-acetyltransferase / Maltose transacetylase


Mass: 21190.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: maa, ylaD, b0459, JW0448 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P77791, maltose O-acetyltransferase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% Poly Ethylene glycol 3350, 0.1M Tris (pH 8.0), 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 78711 / % possible obs: 99.5 % / Redundancy: 5.6 % / Rpim(I) all: 0.029 / Net I/σ(I): 34.66
Reflection shellResolution: 1.34→1.36 Å / Num. unique obs: 3791 / Rpim(I) all: 0.187

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IC7

2ic7


Resolution: 1.34→26.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.882 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 3885 5 %RANDOM
Rwork0.17145 ---
obs0.17239 74382 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0.12 Å2-0 Å2
2---0.24 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: 1 / Resolution: 1.34→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 16 297 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172594
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.663908
X-RAY DIFFRACTIONr_angle_other_deg1.0491.6416066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7745362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45221.646158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84215462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2811524
X-RAY DIFFRACTIONr_chiral_restr0.3130.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023276
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2771.2961456
X-RAY DIFFRACTIONr_mcbond_other1.2711.2941454
X-RAY DIFFRACTIONr_mcangle_it1.7951.9431814
X-RAY DIFFRACTIONr_mcangle_other1.7971.9441815
X-RAY DIFFRACTIONr_scbond_it2.6221.6311419
X-RAY DIFFRACTIONr_scbond_other2.6221.6311419
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9912.3262093
X-RAY DIFFRACTIONr_long_range_B_refined4.8816.7623160
X-RAY DIFFRACTIONr_long_range_B_other4.83916.3983102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.34→1.375 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 240 -
Rwork0.25 5418 -
obs--96.54 %

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