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

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Basic information

Entry
Database: PDB / ID: 4wzy
TitleStructure of mycobacterial maltokinase, the missing link in the essential GlgE-pathway (ATP complex)
ComponentsMaltokinase
KeywordsTRANSFERASE / Maltose / Glycogen / ATP
Function / homology
Function and homology information


maltokinase / trehalose biosynthetic process / carbohydrate phosphorylation / glycogen biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Maltokinase N-terminal cap domain / Maltokinase N-terminal cap domain / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphotransferase enzyme family / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Maltokinase
Similarity search - Component
Biological speciesMycobacterium vanbaalenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsFraga, J. / Empadinhas, N. / Pereira, P.J.B. / Macedo-Ribeiro, S.
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
DepositionNov 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)50,2783
Polymers49,7471
Non-polymers5312
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-12 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.991, 73.767, 107.426
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-607-

HOH

21A-661-

HOH

31A-694-

HOH

41A-725-

HOH

51A-753-

HOH

61A-755-

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(DE3) (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: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Same as entry 4U98.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 54657 / % possible obs: 96.8 % / Redundancy: 4.7 % / Rsym value: 0.08 / Net I/σ(I): 10.7
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.72 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U94

4u94


Resolution: 1.71→47.903 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 2773 5.08 %
Rwork0.1766 --
obs0.178 54627 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→47.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 24 499 4003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073647
X-RAY DIFFRACTIONf_angle_d1.0364981
X-RAY DIFFRACTIONf_dihedral_angle_d11.9361341
X-RAY DIFFRACTIONf_chiral_restr0.043548
X-RAY DIFFRACTIONf_plane_restr0.005665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.73950.33891120.30042585X-RAY DIFFRACTION100
1.7395-1.77110.29931350.27072541X-RAY DIFFRACTION100
1.7711-1.80520.29471380.25882573X-RAY DIFFRACTION100
1.8052-1.84210.24851340.24082549X-RAY DIFFRACTION99
1.8421-1.88210.27711450.23732553X-RAY DIFFRACTION100
1.8821-1.92590.27111390.21862564X-RAY DIFFRACTION100
1.9259-1.97410.26781510.20882561X-RAY DIFFRACTION100
1.9741-2.02740.24511460.2042544X-RAY DIFFRACTION100
2.0274-2.08710.23941360.20092559X-RAY DIFFRACTION100
2.0871-2.15450.2061360.18542600X-RAY DIFFRACTION100
2.1545-2.23150.18871500.17552559X-RAY DIFFRACTION99
2.2315-2.32080.2241330.17112588X-RAY DIFFRACTION100
2.3208-2.42640.19051410.16762584X-RAY DIFFRACTION100
2.4264-2.55430.19851320.17542618X-RAY DIFFRACTION100
2.5543-2.71440.18411370.16852584X-RAY DIFFRACTION100
2.7144-2.92390.20461400.17332603X-RAY DIFFRACTION100
2.9239-3.21810.1991370.17212628X-RAY DIFFRACTION100
3.2181-3.68360.19481380.16272631X-RAY DIFFRACTION99
3.6836-4.64040.16091370.14022658X-RAY DIFFRACTION99
4.6404-47.92140.1891560.16362772X-RAY DIFFRACTION99
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)
12.0798-0.12630.40531.3506-0.62342.4315-0.00760.20540.3867-0.18310.03740.0119-0.2233-0.0733-0.0470.1604-0.01140.0230.17670.00430.227-65.414419.9747100.8739
21.37530.31960.35851.32040.63651.5110.0097-0.0324-0.01010.0378-0.0212-0.0755-0.0986-0.0160.00660.11440.012-0.00440.09330.01290.1019-38.993219.7431121.6711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 209 )
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 452 )

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