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

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Basic information

Entry
Database: PDB / ID: 6jdc
TitleCrystal structure of N-acetyl mannosmaine kinase in complex with ManNAc from Haemophilus influenzae
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-acetylneuraminate catabolic process / zinc ion binding / ATP binding
Similarity search - Function
N-acetylmannosamine kinase, bacterial / : / 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
2-acetamido-2-deoxy-alpha-D-mannopyranose / N-acetylmannosamine kinase
Similarity search - Component
Biological speciesHaemophilus influenzae 86-028NP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 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 1.1Jul 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)31,2073
Polymers30,9201
Non-polymers2872
Water99155
1
A: N-acetylmannosamine kinase
hetero molecules

A: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4146
Polymers61,8402
Non-polymers5734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area4130 Å2
ΔGint-8 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.102, 91.102, 184.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-425-

HOH

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Components

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


Mass: 30920.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae 86-028NP (bacteria)
Strain: 86-028NP / Gene: nanK / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QP43, 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: isolated from a genetically manipulated source
Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M sodium malonate 7.0, 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.865 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.865 Å / Relative weight: 1
ReflectionResolution: 2.22→46.01 Å / Num. obs: 19197 / % possible obs: 98.1 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.042 / Rrim(I) all: 0.084 / Net I/σ(I): 11.3 / Num. measured all: 69837 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.22-2.292.90.4316610.3040.2830.51893.8
8.87-46.013.40.0213440.9990.0120.02493.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3211: ???refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDB

6jdb


Resolution: 2.271→46.008 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 27.59
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2663 909 5.07 %
Rwork0.2167 --
obs0.2191 17926 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.09 Å2 / Biso mean: 44.5861 Å2 / Biso min: 23.67 Å2
Refinement stepCycle: final / Resolution: 2.271→46.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 16 55 2053
Biso mean--32.5 42.38 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2713-2.41360.36691560.32212712286896
2.4136-2.59990.32331460.28272789293597
2.5999-2.86160.31251560.25432792294898
2.8616-3.27550.29011610.23062847300899
3.2755-4.12640.27161420.19672913305599
4.1264-46.01770.20841480.1812964311297

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