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

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Basic information

Entry
Database: PDB / ID: 6jdb
TitleCrystal structure of N-acetyl mannosmaine kinase in complex with ManNAc-6P and ADP from Haemophilus influenzae
ComponentsN-acetylmannosamine kinase
KeywordsSUGAR BINDING PROTEIN / Kinase / ManNAc binding protein / two domain protein / phosphorylation
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 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
ADENOSINE-5'-DIPHOSPHATE / Chem-BMX / N-acetylmannosamine kinase
Similarity search - Component
Biological speciesHaemophilus influenzae 86-028NP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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)31,7704
Polymers30,9761
Non-polymers7943
Water21612
1
A: N-acetylmannosamine kinase
hetero molecules

A: N-acetylmannosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5408
Polymers61,9532
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area4570 Å2
ΔGint-37 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.591, 92.591, 183.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 30976.268 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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Sugar ChemComp-BMX / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose / 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE / N-acetyl-6-O-phosphono-alpha-D-mannosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-ManpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium phosphate monobasic, 0.1M Tris pH 8.5, 50% v/v MPD

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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 A
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.64→46.3 Å / Num. obs: 12021 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.043 / Rrim(I) all: 0.104 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.64-2.776.20.94715280.8280.4121.03598
8.77-46.34.80.0323860.9990.0170.03798.3

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX(1.14_3211: ???)refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDA

6jda


Resolution: 2.65→29.28 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.9
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2756 572 4.8 %
Rwork0.2135 --
obs0.2165 11928 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.79 Å2 / Biso mean: 64.7796 Å2 / Biso min: 34.82 Å2
Refinement stepCycle: final / Resolution: 2.65→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 47 12 2234
Biso mean--69.93 57.78 -
Num. residues----290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6501-2.91650.40751390.30352774291399
2.9165-3.33810.30321500.260627892939100
3.3381-4.20360.29161330.213728382971100
4.2036-29.28160.23841500.18452955310599

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