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- PDB-4wh1: N-Acetylhexosamine 1-kinase (ligand free) -

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Basic information

Entry
Database: PDB / ID: 4wh1
TitleN-Acetylhexosamine 1-kinase (ligand free)
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 / ATP binding
Similarity search - Function
: / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / N-acetylhexosamine 1-kinase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. longum JCM 1217 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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 11, 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 / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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
A: N-acetylhexosamine 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1503
Polymers40,9981
Non-polymers1522
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.164, 88.136, 105.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40997.895 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
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-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 25915 / % possible obs: 98.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000(phenix.refine: 1.8.2_1309)data processing
PHENIXphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
Cootrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→40.648 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 2000 7.73 %
Rwork0.207 --
obs0.2104 25858 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→40.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 10 128 2907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072835
X-RAY DIFFRACTIONf_angle_d0.9673842
X-RAY DIFFRACTIONf_dihedral_angle_d13.341020
X-RAY DIFFRACTIONf_chiral_restr0.067432
X-RAY DIFFRACTIONf_plane_restr0.005503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0343-2.08520.35291270.26561517X-RAY DIFFRACTION89
2.0852-2.14160.29031450.24381719X-RAY DIFFRACTION100
2.1416-2.20460.29171430.21761710X-RAY DIFFRACTION100
2.2046-2.27570.26651450.22361735X-RAY DIFFRACTION100
2.2757-2.3570.30951430.2171696X-RAY DIFFRACTION100
2.357-2.45140.32081440.21931732X-RAY DIFFRACTION100
2.4514-2.5630.2491450.21671725X-RAY DIFFRACTION100
2.563-2.69810.25021460.21531738X-RAY DIFFRACTION100
2.6981-2.86710.24821450.21861729X-RAY DIFFRACTION100
2.8671-3.08840.26471460.20591749X-RAY DIFFRACTION100
3.0884-3.3990.24611450.21441728X-RAY DIFFRACTION99
3.399-3.89050.22391470.1921743X-RAY DIFFRACTION98
3.8905-4.90030.22281410.18021687X-RAY DIFFRACTION94
4.9003-40.65580.24131380.21111650X-RAY DIFFRACTION87

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