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- PDB-4u94: Structure of mycobacterial maltokinase, the missing link in the e... -

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Basic information

Entry
Database: PDB / ID: 4u94
TitleStructure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway
ComponentsMaltokinase
KeywordsTRANSFERASE / Mycobacterium vanbalenii / Maltokinase / Maltose / Glycogen / AppCp
Function / homology
Function and homology information


maltokinase / carbohydrate phosphorylation / trehalose biosynthetic process / glycogen biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Maltokinase N-terminal cap domain / Maltokinase N-terminal cap domain / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium vanbaalenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.473 Å
AuthorsFraga, J. / Empadinhas, N. / Pereira, P.J.B. / Macedo-Ribeiro, S.
Funding support Portugal, 4items
OrganizationGrant numberCountry
FCTFCOMP-01-0124-FEDER-028359 Portugal
FCTFCOMP-01-0124-FEDER-014321 Portugal
FCTFCOMP-01-0124-FEDER-014187 Portugal
ON.2 - O Novo NorteNORTE-07-0124-000002 - Host-Pathogen Interactions Portugal
CitationJournal: Sci Rep / Year: 2015
Title: Structure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway.
Authors: Fraga, J. / Maranha, A. / Mendes, V. / Pereira, P.J. / Empadinhas, N. / Macedo-Ribeiro, S.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Maltokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7712
Polymers49,7471
Non-polymers241
Water10,341574
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.947, 73.409, 106.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-726-

HOH

31A-732-

HOH

41A-767-

HOH

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Components

#1: Protein Maltokinase / MaK / Maltose-1-phosphate synthase


Mass: 49746.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium vanbaalenii (bacteria) / Strain: DSM 7251 / PYR-1 / Gene: mak, Mvan_5735 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A1TH50, maltokinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MOPS/sodium HEPES pH 7.5, 0.12 M ethylene glycols (0.03M each of di-ethyleneglycol, tri-ethyleneglycol, tetra-ethyleneglycol, and penta-ethyleneglycol), 30% PEG 500MME/PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.47→40.741 Å / Num. obs: 84256 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rsym value: 0.057 / Net I/σ(I): 24.6
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 7.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.473→40.741 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1799 4204 4.99 %
Rwork0.1396 --
obs0.1416 84211 99.86 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.473→40.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 1 574 4055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143665
X-RAY DIFFRACTIONf_angle_d1.4155013
X-RAY DIFFRACTIONf_dihedral_angle_d12.2691358
X-RAY DIFFRACTIONf_chiral_restr0.091552
X-RAY DIFFRACTIONf_plane_restr0.008676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4734-1.49020.18611300.11722559X-RAY DIFFRACTION96
1.4902-1.50770.17921430.11412632X-RAY DIFFRACTION100
1.5077-1.52610.15831390.10872633X-RAY DIFFRACTION100
1.5261-1.54540.16541280.10692635X-RAY DIFFRACTION100
1.5454-1.56580.14111380.09982644X-RAY DIFFRACTION100
1.5658-1.58720.18121360.10052637X-RAY DIFFRACTION100
1.5872-1.60990.16791210.10182664X-RAY DIFFRACTION100
1.6099-1.63390.15621630.09792612X-RAY DIFFRACTION100
1.6339-1.65940.1591510.10262643X-RAY DIFFRACTION100
1.6594-1.68660.1511270.10322633X-RAY DIFFRACTION100
1.6866-1.71570.15651420.10152649X-RAY DIFFRACTION100
1.7157-1.74690.16331350.10632671X-RAY DIFFRACTION100
1.7469-1.78050.16111520.10992629X-RAY DIFFRACTION100
1.7805-1.81690.19511430.11152626X-RAY DIFFRACTION100
1.8169-1.85640.17311270.12032662X-RAY DIFFRACTION100
1.8564-1.89960.16951230.11892688X-RAY DIFFRACTION100
1.8996-1.94710.16581480.12052633X-RAY DIFFRACTION100
1.9471-1.99970.15951300.12562652X-RAY DIFFRACTION100
1.9997-2.05860.17751390.13142701X-RAY DIFFRACTION100
2.0586-2.1250.17321300.12672651X-RAY DIFFRACTION100
2.125-2.20090.16481250.12482685X-RAY DIFFRACTION100
2.2009-2.28910.16361580.13112660X-RAY DIFFRACTION100
2.2891-2.39320.18821530.13982656X-RAY DIFFRACTION100
2.3932-2.51940.17621340.14242700X-RAY DIFFRACTION100
2.5194-2.67720.19331540.14952661X-RAY DIFFRACTION100
2.6772-2.88390.18361360.16392722X-RAY DIFFRACTION100
2.8839-3.1740.18911540.16532693X-RAY DIFFRACTION100
3.174-3.6330.18791390.15562728X-RAY DIFFRACTION100
3.633-4.57620.18281330.14972778X-RAY DIFFRACTION100
4.5762-40.75660.20611730.17512870X-RAY DIFFRACTION100

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