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- PDB-6ppy: Crystal structure of NeuNAc oxime complexed with NeuB, an N-acety... -

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Basic information

Entry
Database: PDB / ID: 6ppy
TitleCrystal structure of NeuNAc oxime complexed with NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis
ComponentsN-acetylneuraminate synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / inhibitor complex / N-acetyl-neuraminate synthase / NeuNAc oxime
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 / SAF domain / 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. ...N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / 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
Chem-OVY / N-acetylneuraminate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRosanally, A.Z. / Junop, M.J. / Berti, P.J.
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)38,7202
Polymers38,3961
Non-polymers3241
Water6,990388
1
A: N-acetylneuraminate synthase
hetero molecules

A: N-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4404
Polymers76,7912
Non-polymers6492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7370 Å2
ΔGint-43 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.110, 76.040, 77.570
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-OVY / (2E,4S,5R,6R,7S,8R)-5-(acetylamino)-4,6,7,8,9-pentahydroxy-2-(hydroxyimino)nonanoic acid (non-preferred name)


Mass: 324.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H20N2O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.75 M malic acid, pH 6.2 10 mM MgCl2 10 mM NeuNAc 10 mM hydroxylamine hydrochloride

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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→46.51 Å / Num. obs: 23512 / % possible obs: 98.5 % / Redundancy: 3.95 % / Biso Wilson estimate: 23.08 Å2 / Rmerge(I) obs: 0.116 / Χ2: 0.98 / Net I/av σ(I): 7.8 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.97 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1587 / Χ2: 1.13 / % possible all: 97.4

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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→46.17 Å / SU ML: 0.2586 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5809
RfactorNum. reflection% reflection
Rfree0.2489 1209 5.14 %
Rwork0.1672 --
obs0.1714 23508 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 2→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 22 388 3081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712746
X-RAY DIFFRACTIONf_angle_d0.80483708
X-RAY DIFFRACTIONf_chiral_restr0.0505414
X-RAY DIFFRACTIONf_plane_restr0.0048488
X-RAY DIFFRACTIONf_dihedral_angle_d10.90932317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.32811060.26362422X-RAY DIFFRACTION97.49
2.08-2.170.31541460.242396X-RAY DIFFRACTION97.1
2.17-2.290.31161320.22392421X-RAY DIFFRACTION98.15
2.29-2.430.29341490.20722430X-RAY DIFFRACTION98.47
2.43-2.620.28971440.19392458X-RAY DIFFRACTION98.71
2.62-2.880.25231310.18462483X-RAY DIFFRACTION99.32
2.88-3.30.27591440.16142510X-RAY DIFFRACTION99.59
3.3-4.160.21321310.11772540X-RAY DIFFRACTION99.48
4.16-46.180.16431260.12612639X-RAY DIFFRACTION97.98
Refinement TLS params.Method: refined / Origin x: -21.1346954873 Å / Origin y: 4.41387238964 Å / Origin z: -16.916293827 Å
111213212223313233
T0.164882870322 Å20.0153440238727 Å20.00758891719902 Å2-0.189624662121 Å2-0.0121568716876 Å2--0.167048424745 Å2
L0.256931296583 °20.348490413657 °20.150505163747 °2-0.830842699102 °20.245896851476 °2--0.217437376477 °2
S0.0140443477048 Å °0.0244752019666 Å °-0.0219541228944 Å °-0.0149188961065 Å °-0.00464439331679 Å °-0.0425576589815 Å °0.000606091958719 Å °0.00929892381634 Å °-0.00741516389733 Å °
Refinement TLS groupSelection details: all

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