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- PDB-6jda: Crystal structure of N-acetyl mannosmaine kinase in complex with ... -

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Basic information

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


N-acylmannosamine kinase / N-acylmannosamine kinase activity / N-acetylmannosamine metabolic process / 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
2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetylmannosamine kinase / N-acetylmannosamine kinase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionJan 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 16, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0684
Polymers30,6891
Non-polymers3793
Water1267
1
A: N-acetylmannosamine kinase
hetero molecules

A: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1358
Polymers61,3782
Non-polymers7576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4910 Å2
ΔGint-21 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.816, 173.732, 48.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 30689.037 Da / Num. of mol.: 1
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, UniProt: Q9CKB3*PLUS, N-acylmannosamine kinase
#2: Sugar ChemComp-BM3 / 2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetyl-alpha-D-mannosamine / 2-acetamido-2-deoxy-alpha-D-mannose / 2-acetamido-2-deoxy-D-mannose / 2-acetamido-2-deoxy-mannose / 2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-MANNOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M lithium citrate tribasic tetrahydrate, 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.9→48.06 Å / Num. obs: 9983 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Net I/σ(I): 13.4 / Num. measured all: 62338 / Scaling rejects: 28
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.447 / Num. measured all: 9925 / Num. unique obs: 1573 / CC1/2: 0.881 / Rpim(I) all: 0.196 / Rrim(I) all: 0.489 / Net I/σ(I) obs: 3.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2aa4

2aa4


Resolution: 2.9→44.559 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 471 4.72 %
Rwork0.1939 9499 -
obs0.1966 9970 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.53 Å2 / Biso mean: 63.5832 Å2 / Biso min: 29.41 Å2
Refinement stepCycle: final / Resolution: 2.9→44.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 22 7 2182
Biso mean--57.68 50.56 -
Num. residues----291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9002-3.31970.39631310.27731313262100
3.3197-4.1820.26611670.202231373304100
4.182-44.56380.20571730.16713231340498

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