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- PDB-6ppz: Crystal structure of NeuB, an N-acetylneuraminate synthase from N... -

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Basic information

Entry
Database: PDB / ID: 6ppz
TitleCrystal structure of NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis, in complex with manganese, inorganic phosphate, and N-acetylmannosamine (NeuB.Mn2+.Pi.ManNAc)
ComponentsN-acetylneuraminate synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / Siac / N-acetylneuraminate synthase / phosphate / N-acetylmannosamine
Function / homology
Function and homology information


N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / N-acylneuraminate-9-phosphate synthase activity / glycosylation / carbohydrate biosynthetic process / metal ion binding
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF domain / SAF / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily ...N-acetylneuraminic acid synthase, N-terminal / NeuB family / SAF domain / SAF domain / SAF / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / 2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE / PHOSPHATE ION / N-acetylneuraminate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBerti, P.J. / Junop, M.S.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-64422 Canada
Canadian Institutes of Health Research (CIHR)MOP-89903 Canada
CitationJournal: Biochemistry / Year: 2019
Title: NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB.
Authors: Popovic, V. / Morrison, E. / Rosanally, A.Z. / Balachandran, N. / Senson, A.W. / Szabla, R. / Junop, M.S. / Berti, P.J.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7674
Polymers38,3961
Non-polymers3713
Water3,441191
1
A: N-acetylneuraminate synthase
hetero molecules

A: N-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5348
Polymers76,7912
Non-polymers7426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area8200 Å2
ΔGint-73 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 75.860, 77.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein N-acetylneuraminate synthase / SynC protein


Mass: 38395.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: synC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2VFG5, N-acetylneuraminate synthase
#2: Chemical ChemComp-MN9 / 2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE


Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.75 M malic acid, pH 6.2 2M NaH2PO4, pH 6.2, 10 mM MnCl2, 10 mM ManNAc, 10 mM NeuNAc oxime, 10 mM NH2OH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 6, 2007
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→46.46 Å / Num. obs: 13862 / % possible obs: 99.2 % / Redundancy: 3.93 % / Biso Wilson estimate: 28.56 Å2 / Rmerge(I) obs: 0.109 / Χ2: 0.95 / Net I/σ(I): 9.1
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4 / Num. unique obs: 1280 / Χ2: 1.07 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XUZ

1xuz


Resolution: 2.4→29.69 Å / SU ML: 0.3626 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.3329
RfactorNum. reflection% reflection
Rfree0.2652 706 5.09 %
Rwork0.1787 --
obs0.183 13859 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.93 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 21 191 2879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762732
X-RAY DIFFRACTIONf_angle_d0.8653688
X-RAY DIFFRACTIONf_chiral_restr0.0514412
X-RAY DIFFRACTIONf_plane_restr0.0063483
X-RAY DIFFRACTIONf_dihedral_angle_d15.01011663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.580.34431560.2472561X-RAY DIFFRACTION99.12
2.58-2.840.32991330.23442602X-RAY DIFFRACTION100
2.84-3.250.32921550.20682613X-RAY DIFFRACTION99.96
3.25-4.10.2281370.14792650X-RAY DIFFRACTION99.96
4.1-29.690.19821250.14512727X-RAY DIFFRACTION97.27

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