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- PDB-4wh3: N-acetylhexosamine 1-kinase in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 4wh3
TitleN-acetylhexosamine 1-kinase in complex with ATP
ComponentsN-acetylhexosamine 1-kinase
KeywordsTRANSFERASE / NahK / anomeric kinase / APH / open conformation
Function / homology
Function and homology information


N-acetylhexosamine 1-kinase / homoserine kinase activity / phosphotransferase activity, alcohol group as acceptor / threonine biosynthetic process / carbohydrate metabolic process / phosphorylation / ATP binding
Similarity search - Function
Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / N-acetylhexosamine 1-kinase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum JCM 1217 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSato, M. / Arakawa, T. / Nam, Y.W. / Nishimoto, M. / Kitaoka, M. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries Japan
Citation
Journal: Biochim.Biophys.Acta / Year: 2015
Title: Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase
Authors: Sato, M. / Arakawa, T. / Nam, Y.W. / Nishimoto, M. / Kitaoka, M. / Fushinobu, S.
#1: Journal: Appl. Environ. Microbiol. / Year: 2007
Title: Identification of N-acetylhexosamine 1-kinase in the complete lacto-N-biose I/galacto-N-biose metabolic pathway in Bifidobacterium longum.
Authors: Nishimoto, M. / Kitaoka, M.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylhexosamine 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,65011
Polymers41,5141
Non-polymers1,13610
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-25 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.030, 88.471, 105.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetylhexosamine 1-kinase / N-acetylgalactosamine/N-acetylglucosamine 1-kinase


Mass: 41513.734 Da / Num. of mol.: 1 / Mutation: D7V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum JCM 1217 (bacteria)
Gene: nahK, lnpB, BLLJ_1622 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3) / References: UniProt: E8MF12, N-acetylhexosamine 1-kinase

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Non-polymers , 5 types, 299 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8000, magnesium acetate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 73240 / % possible obs: 99 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 43.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 4.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIXphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
Cootrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→32.604 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 3737 5.11 %
Rwork0.1889 --
obs0.1906 73176 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072905
X-RAY DIFFRACTIONf_angle_d1.0673936
X-RAY DIFFRACTIONf_dihedral_angle_d15.8741046
X-RAY DIFFRACTIONf_chiral_restr0.075438
X-RAY DIFFRACTIONf_plane_restr0.004508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7964-1.81910.31021320.24092408X-RAY DIFFRACTION93
1.8191-1.8430.34461390.23172624X-RAY DIFFRACTION99
1.843-1.86830.27221390.21522579X-RAY DIFFRACTION100
1.8683-1.8950.21731450.21572602X-RAY DIFFRACTION99
1.895-1.92330.27591410.22082596X-RAY DIFFRACTION99
1.9233-1.95330.21681390.21232553X-RAY DIFFRACTION100
1.9533-1.98530.27921430.21332620X-RAY DIFFRACTION100
1.9853-2.01960.23441410.20372608X-RAY DIFFRACTION100
2.0196-2.05630.23521410.20212578X-RAY DIFFRACTION100
2.0563-2.09580.2441360.20432644X-RAY DIFFRACTION100
2.0958-2.13860.24251390.20072512X-RAY DIFFRACTION100
2.1386-2.18510.24361420.20532657X-RAY DIFFRACTION100
2.1851-2.23590.26791360.20732588X-RAY DIFFRACTION100
2.2359-2.29180.23671390.1992594X-RAY DIFFRACTION100
2.2918-2.35370.22871390.21052576X-RAY DIFFRACTION100
2.3537-2.4230.25481370.20392615X-RAY DIFFRACTION100
2.423-2.50120.23071390.2042596X-RAY DIFFRACTION100
2.5012-2.59050.21581420.19262635X-RAY DIFFRACTION100
2.5905-2.69420.24551360.192531X-RAY DIFFRACTION99
2.6942-2.81670.2171440.19022598X-RAY DIFFRACTION100
2.8167-2.96520.24051410.19322569X-RAY DIFFRACTION99
2.9652-3.15080.20161380.18562584X-RAY DIFFRACTION99
3.1508-3.39380.19851380.18312593X-RAY DIFFRACTION99
3.3938-3.73490.24191330.16872517X-RAY DIFFRACTION98
3.7349-4.27440.19241370.15672546X-RAY DIFFRACTION98
4.2744-5.38130.16751350.16732513X-RAY DIFFRACTION96
5.3813-32.60970.20361260.18772403X-RAY DIFFRACTION92

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