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- PDB-5nck: The Crystal Structure of N-acetylmannosamine kinase in Fusobacter... -

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Basic information

Entry
Database: PDB / ID: 5nck
TitleThe Crystal Structure of N-acetylmannosamine kinase in Fusobacterium nucleatum
ComponentsN-acetylmannosamine kinase
KeywordsTRANSFERASE / N-acetylmannosamine kinase / zinc-binding motif / ROK family / sialic acid
Function / homology
Function and homology information


N-acylmannosamine kinase activity / N-acylmannosamine kinase
Similarity search - Function
: / ROK family signature. / ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylmannosamine kinase
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.23 Å
AuthorsCaing-Carlsson, R. / Sharma, A. / Friemann, R. / Ramaswamy, S.
Funding support India, Sweden, 4items
OrganizationGrant numberCountry
Department of BiotechnologyBT/IN/Sweden/41/SR/2013 India
Department of BiotechnologyBT/PR5081/INF/22/156/2012 India
Vinnova2013-04655 Sweden
Swedish Research Council2011-5790 Sweden
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of N-acetylmannosamine kinase from Fusobacterium nucleatum.
Authors: Caing-Carlsson, R. / Goyal, P. / Sharma, A. / Ghosh, S. / Setty, T.G. / North, R.A. / Friemann, R. / Ramaswamy, S.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 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

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Assembly

Deposited unit
A: N-acetylmannosamine kinase
B: N-acetylmannosamine kinase


Theoretical massNumber of molelcules
Total (without water)63,8062
Polymers63,8062
Non-polymers00
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-22 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.520, 126.520, 108.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein N-acetylmannosamine kinase


Mass: 31903.076 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: FN1474 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RDN7, N-acylmannosamine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000,0.2 M lithium sulfate monohydrate, 0.1 M tris hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→54.785 Å / Num. obs: 54608 / % possible obs: 99 % / Redundancy: 2.7 % / Net I/σ(I): 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.23→48.936 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 2384 4.83 %
Rwork0.1768 --
obs0.1788 49331 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→48.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 0 0 478 4964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014548
X-RAY DIFFRACTIONf_angle_d1.0896118
X-RAY DIFFRACTIONf_dihedral_angle_d14.832734
X-RAY DIFFRACTIONf_chiral_restr0.062704
X-RAY DIFFRACTIONf_plane_restr0.007780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.27550.35551280.30552726X-RAY DIFFRACTION100
2.2755-2.3250.30791280.26582754X-RAY DIFFRACTION100
2.325-2.37910.31871550.2442720X-RAY DIFFRACTION100
2.3791-2.43860.29241570.23342730X-RAY DIFFRACTION100
2.4386-2.50450.25821130.21342730X-RAY DIFFRACTION100
2.5045-2.57820.26321670.21332751X-RAY DIFFRACTION100
2.5782-2.66140.25771510.20412711X-RAY DIFFRACTION100
2.6614-2.75650.2951460.19522737X-RAY DIFFRACTION100
2.7565-2.86690.26371620.17752733X-RAY DIFFRACTION100
2.8669-2.99730.22471670.18582707X-RAY DIFFRACTION100
2.9973-3.15530.23771200.19232798X-RAY DIFFRACTION100
3.1553-3.3530.18921150.16252778X-RAY DIFFRACTION100
3.353-3.61180.20511480.15892755X-RAY DIFFRACTION100
3.6118-3.97510.17581130.15032807X-RAY DIFFRACTION100
3.9751-4.550.17191510.1362783X-RAY DIFFRACTION100
4.55-5.73110.19861370.14412823X-RAY DIFFRACTION100
5.7311-48.94790.15131260.16052904X-RAY DIFFRACTION99

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