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- PDB-5lky: X-ray crystal structure of N-acetylneuraminic acid lyase in compl... -

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Basic information

Entry
Database: PDB / ID: 5lky
TitleX-ray crystal structure of N-acetylneuraminic acid lyase in complex with pyruvate, with the phenylalanine at position 190 replaced with the non-canonical amino acid dihydroxypropylcysteine.
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / aldolase / non-canonical amino acid / TIM barrel
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
N-acetylneuraminate lyase / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWindle, C.L. / Trinh, C.H. / Pearson, A.R. / Nelson, A.S. / Berry, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N002091/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/F01614X/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Extending enzyme molecular recognition with an expanded amino acid alphabet.
Authors: Windle, C.L. / Simmons, K.J. / Ault, J.R. / Trinh, C.H. / Nelson, A. / Pearson, A.R. / Berry, A.
History
DepositionJul 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,7466
Polymers136,5344
Non-polymers2122
Water7,458414
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-45 kcal/mol
Surface area39330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.490, 134.300, 79.460
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-acetylneuraminate lyase / Neu5Ac lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate ...Neu5Ac lyase / N-acetylneuraminate pyruvate-lyase / N-acetylneuraminic acid aldolase / Sialate lyase / Sialic acid aldolase / Sialic acid lyase


Mass: 34133.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Gene: nanA, SAOUHSC_00295 / Plasmid: pKK223-3 / Organ (production host): NA / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): NA / References: UniProt: Q2G160, N-acetylneuraminate lyase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.07 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350 (18-28%), 200mM NaCl, 100mM Tric/HCl pH 7.0-8.5
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2013 / Details: Mirrors
RadiationMonochromator: Si (III) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→75.54 Å / Num. obs: 120355 / % possible obs: 99.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3 / CC1/2: 0.811 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ah7

4ah7


Resolution: 1.7→75.53 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.376 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20254 6056 5 %RANDOM
Rwork0.1737 ---
obs0.17515 114242 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.34 Å2
2---0.16 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.7→75.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9275 0 14 414 9703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199490
X-RAY DIFFRACTIONr_bond_other_d0.0040.029142
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.97612840
X-RAY DIFFRACTIONr_angle_other_deg1.0483.00421030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89551173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93725.339472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.089151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0061544
X-RAY DIFFRACTIONr_chiral_restr0.0840.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022156
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2882.1284662
X-RAY DIFFRACTIONr_mcbond_other1.2882.1284661
X-RAY DIFFRACTIONr_mcangle_it1.9633.1875824
X-RAY DIFFRACTIONr_mcangle_other1.9633.1875825
X-RAY DIFFRACTIONr_scbond_it2.0582.4394828
X-RAY DIFFRACTIONr_scbond_other2.0572.4394828
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3313.5487010
X-RAY DIFFRACTIONr_long_range_B_refined4.37817.50411082
X-RAY DIFFRACTIONr_long_range_B_other4.37817.50711083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 406 -
Rwork0.261 7782 -
obs--91.6 %

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