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- PDB-4o7o: Crystal structure of Mycobacterium tuberculosis maltose kinase MaK -

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Basic information

Entry
Database: PDB / ID: 4o7o
TitleCrystal structure of Mycobacterium tuberculosis maltose kinase MaK
ComponentsMaltokinase
KeywordsTRANSFERASE / maltose kinase / kinase / ATP binding / maltose binding
Function / homology
Function and homology information


maltokinase / trehalose biosynthetic process / carbohydrate phosphorylation / glycogen biosynthetic process / kinase activity / ATP binding / plasma membrane / cytosol
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 / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4006 Å
AuthorsLi, J. / Guan, X.T. / Rao, Z.H.
CitationJournal: Sci Rep / Year: 2014
Title: Homotypic dimerization of a maltose kinase for molecular scaffolding.
Authors: Li, J. / Guan, X. / Shaw, N. / Chen, W. / Dong, Y. / Xu, X. / Li, X. / Rao, Z.
History
DepositionDec 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltokinase
B: Maltokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9603
Polymers99,8642
Non-polymers961
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-17 kcal/mol
Surface area38000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.610, 96.610, 459.697
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 49931.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: mak, Rv0127 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O07177, maltokinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 1M (NH4)2SO4, 1% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 12.4 % / Number: 282429 / Rmerge(I) obs: 0.138 / Χ2: 1.07 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 22780 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.895099.510.0731.05614.2
5.476.8999.910.1161.04712.5
4.785.4799.710.1371.06711.9
4.344.7899.410.1571.08711.7
4.034.3499.410.2021.08611.9
3.794.0399.110.2931.06712
3.63.7999.110.2831.04612.3
3.453.69910.4871.08812.4
3.313.4599.110.6151.08112.5
3.23.3199.110.7531.05712.5
ReflectionResolution: 2.4→50 Å / Num. all: 51256 / Num. obs: 51256 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 35.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementResolution: 2.4006→38.308 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8224 / SU ML: 0.37 / σ(F): 0 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 2543 5.06 %
Rwork0.2066 47694 -
obs0.2085 50237 98.28 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.405 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 162.47 Å2 / Biso mean: 64.8513 Å2 / Biso min: 21.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.8817 Å20 Å2-0 Å2
2--2.8817 Å2-0 Å2
3----5.7635 Å2
Refinement stepCycle: LAST / Resolution: 2.4006→38.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6839 0 5 154 6998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177330
X-RAY DIFFRACTIONf_angle_d1.2499534
X-RAY DIFFRACTIONf_chiral_restr0.0841069
X-RAY DIFFRACTIONf_plane_restr0.0061257
X-RAY DIFFRACTIONf_dihedral_angle_d16.482517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4006-2.44670.351400.26482407254792
2.4467-2.49670.32481310.26452465259694
2.4967-2.55090.30381360.24762517265395
2.5509-2.61030.28521340.23532557269196
2.6103-2.67550.34811360.2582527266397
2.6755-2.74790.34931370.24672596273398
2.7479-2.82870.29951370.24072625276299
2.8287-2.920.28241330.22982631276499
2.92-3.02430.30521580.22792631278999
3.0243-3.14530.28081500.223626252775100
3.1453-3.28840.27141370.218126792816100
3.2884-3.46170.25311260.213527162842100
3.4617-3.67840.23821510.200526582809100
3.6784-3.96210.21151300.198627232853100
3.9621-4.36030.26481340.18427492883100
4.3603-4.99010.17771480.166127662914100
4.9901-6.28250.22651640.212427912955100
6.2825-38.31290.19791610.192930313192100
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)
10.28460.2661-0.15060.52110.17980.4111-0.1483-0.0018-0.05631.34430.3394-0.02240.038-0.27070.13611.1850.2758-0.01080.20620.0750.3078-59.478917.36759.2877
20.7389-0.14450.31830.291-0.26580.2781-0.04040.17620.0935-0.12880.07960.0213-0.1184-0.1427-0.01970.32690.01850.01160.26040.01730.2363-54.49716.5055-13.9962
30.88470.31540.12250.5718-0.12120.4511-0.31680.35320.03390.60320.43470.3084-0.6463-0.50030.0450.44970.32630.12950.23340.19180.2414-69.944138.3868-19.3929
40.2992-0.23270.21990.2884-0.08160.56060.26510.0633-0.2329-0.260.01190.07230.51840.1713-0.09840.45610.0461-0.10360.2591-0.02140.2627-36.98892.297-30.1917
50.58120.00980.25960.0724-0.14690.51730.1912-0.1088-0.08710.0157-0.1564-0.034-0.079-0.05780.00740.3365-0.0019-0.0690.2210.05250.2763-37.260210.7216-8.3908
60.66770.17540.18010.8236-0.26180.7033-0.00560.06160.04710.0942-0.1516-0.6336-0.08170.10480.06360.3269-0.0731-0.04790.22150.11010.4804-11.409821.0218-10.1303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:124)A6 - 124
2X-RAY DIFFRACTION2chain 'A' and (resseq 125:220)A125 - 220
3X-RAY DIFFRACTION3chain 'A' and (resseq 221:454)A221 - 454
4X-RAY DIFFRACTION4chain 'B' and (resseq 5:124)B5 - 124
5X-RAY DIFFRACTION5chain 'B' and (resseq 125:220)B125 - 220
6X-RAY DIFFRACTION6chain 'B' and (resseq 221:455)B221 - 455

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