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

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Basic information

Entry
Database: PDB / ID: 6ppw
TitleCrystal structure of NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis, in complex with magnesium and malate
ComponentsN-acetylneuraminate synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / N-acetylneuraminate synthase
Function / homology
Function and homology information


N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / N-acylneuraminate-9-phosphate synthase activity / : / 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
D-MALATE / N-acetylneuraminate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRosanally, A.Z. / Junop, M.S. / 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
SupersessionOct 9, 2019ID: 2ZDR
Revision 1.1Oct 9, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
Revision 1.2Oct 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 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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)38,5543
Polymers38,3961
Non-polymers1582
Water5,621312
1
A: N-acetylneuraminate synthase
hetero molecules

A: N-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1086
Polymers76,7912
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8310 Å2
ΔGint-55 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.793, 76.030, 77.370
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 10mM MgCl2 3% (v/v) MPD 1.7M Malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→77.38 Å / Num. obs: 30334 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 20.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.054 / Rrim(I) all: 0.117 / Net I/σ(I): 2.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2959 / CC1/2: 0.641 / Rpim(I) all: 0.409 / Rrim(I) all: 0.882 / % possible all: 99.9

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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: 1.85→29.74 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5966
RfactorNum. reflection% reflection
Rfree0.2227 1533 5.07 %
Rwork0.1781 --
obs0.1803 30218 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.23 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 10 312 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642722
X-RAY DIFFRACTIONf_angle_d0.79613674
X-RAY DIFFRACTIONf_chiral_restr0.0545408
X-RAY DIFFRACTIONf_plane_restr0.005484
X-RAY DIFFRACTIONf_dihedral_angle_d27.63351022
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.26061150.24922560X-RAY DIFFRACTION99.59
1.91-1.980.25971460.19692578X-RAY DIFFRACTION99.93
1.98-2.060.23411570.18952562X-RAY DIFFRACTION99.96
2.06-2.150.23461400.1712565X-RAY DIFFRACTION99.96
2.15-2.260.20711320.17672603X-RAY DIFFRACTION99.96
2.26-2.410.23651360.19432581X-RAY DIFFRACTION99.82
2.41-2.590.27011320.20612591X-RAY DIFFRACTION99.6
2.59-2.850.26641200.2022638X-RAY DIFFRACTION99.96
2.85-3.260.2291610.18112617X-RAY DIFFRACTION100
3.26-4.110.19891500.14942638X-RAY DIFFRACTION100
4.11-29.750.19181440.16172752X-RAY DIFFRACTION98.4

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