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- PDB-6jdh: Crystal structure of N-acetyl mannosmaine kinase from Pasteurella... -

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Basic information

Entry
Database: PDB / ID: 6jdh
TitleCrystal structure of N-acetyl mannosmaine kinase from Pasteurella multocida
ComponentsN-acetylmannosamine kinase
KeywordsSUGAR BINDING PROTEIN / Kinase / ManNAc binding protein / two domain protein
Function / homology
Function and homology information


N-acetylmannosamine metabolic process / N-acylmannosamine kinase activity / N-acylmannosamine kinase / N-acetylneuraminate catabolic process / zinc ion binding / ATP binding
Similarity search - Function
N-acetylmannosamine kinase, bacterial / 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 speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsThanuja, G. / Ramaswamy, S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/IN/Sweden/06/SR/2017-18 India
Department of Biotechnology (India)BT/PR12422/MED/31/287/ 2014 India
CitationJournal: Acs Omega / Year: 2020
Title: Structure and Function of N‐Acetylmannosamine Kinases from Pathogenic Bacteria.
Authors: Thanuja, G. / Ramaswamy, S.
History
DepositionFeb 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0236
Polymers62,7082
Non-polymers3154
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-24 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.336, 126.336, 82.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein N-acetylmannosamine kinase / ManNAc kinase / N-acetyl-D-mannosamine kinase


Mass: 31353.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ROK kinase / Source: (gene. exp.) Pasteurella multocida (bacteria) / Gene: nanK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2K0XYW4, N-acylmannosamine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tascimate 5.0, 20% v/v Isopropanol, 20% w/v PEG 4000 with an additive containing 2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→45.58 Å / Num. obs: 59936 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.027 / Rrim(I) all: 0.085 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.947.71.19338360.7830.4561.27999.5
9.11-45.588.40.0376040.9990.0140.0498.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDA

6jda


Resolution: 1.9→38.565 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.24
RfactorNum. reflection% reflection
Rfree0.23 2997 5.01 %
Rwork0.1964 --
obs0.198 59824 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.61 Å2 / Biso mean: 38.7923 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 1.9→38.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4319 0 30 342 4691
Biso mean--75.38 42.63 -
Num. residues----584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.93130.42141510.38462669282099
1.9313-1.96460.38941440.320226692813100
1.9646-2.00030.30741570.272226702827100
2.0003-2.03880.31051170.254727202837100
2.0388-2.08040.28171570.235926132770100
2.0804-2.12560.31031560.228627152871100
2.1256-2.17510.24911480.233126562804100
2.1751-2.22950.29371200.2327072827100
2.2295-2.28970.27741500.230227132863100
2.2897-2.35710.26151420.218626942836100
2.3571-2.43320.26821250.214327152840100
2.4332-2.52010.29941520.211926712823100
2.5201-2.6210.22351330.218426862819100
2.621-2.74030.26391200.211227482868100
2.7403-2.88470.24151320.217927122844100
2.8847-3.06540.24541420.21627042846100
3.0654-3.30190.21781530.204527262879100
3.3019-3.6340.21351710.183726712842100
3.634-4.15930.19921550.16327462901100
4.1593-5.23820.17821250.149827892914100
5.2382-38.5730.17761470.15752833298099

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