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- PDB-5kzd: N-acetylneuraminate lyase from methicillin-resistant Staphylococc... -

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Basic information

Entry
Database: PDB / ID: 5kzd
TitleN-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus with bound sialic acid alditol
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / TIM-barrel / inhibitor / N-acetylneuraminate lyase
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol / cytoplasm
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
Chem-RCJ / N-acetylneuraminate lyase / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.334 Å
AuthorsNorth, R.A. / Watson, A.J.A. / Pearce, F.G. / Muscroft-Taylor, A.C. / Friemann, R. / Fairbanks, A.J. / Dobson, R.C.J.
CitationJournal: FEBS Lett. / Year: 2016
Title: Structure and inhibition of N-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus.
Authors: North, R.A. / Watson, A.J. / Pearce, F.G. / Muscroft-Taylor, A.C. / Friemann, R. / Fairbanks, A.J. / Dobson, R.C.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)133,5518
Polymers132,3064
Non-polymers1,2454
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9790 Å2
ΔGint-48 kcal/mol
Surface area40810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.477, 109.444, 130.752
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 33076.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: nanA, SAUSA300_0315 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2FJU9, UniProt: Q2G160*PLUS, N-acetylneuraminate lyase
#2: Chemical
ChemComp-RCJ / (2~{S},4~{S},5~{R},6~{R},7~{S},8~{R})-5-acetamido-2,4,6,7,8,9-hexakis(oxidanyl)nonanoic acid


Mass: 311.286 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H21NO9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 3350, sodium chloride, Tris, sialic acid alditols

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.33→38.179 Å / Num. obs: 49980 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 35.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.33-2.417.20.8730.774189.8
9.34-46.226.40.0290.999199.1

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementResolution: 2.334→38.179 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.38
RfactorNum. reflection% reflection
Rfree0.261 2000 4.01 %
Rwork0.1934 --
obs0.1962 49898 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.1 Å2 / Biso mean: 36.4025 Å2 / Biso min: 15.37 Å2
Refinement stepCycle: final / Resolution: 2.334→38.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9080 0 84 177 9341
Biso mean--37.71 33 -
Num. residues----1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099324
X-RAY DIFFRACTIONf_angle_d1.18512592
X-RAY DIFFRACTIONf_chiral_restr0.0461404
X-RAY DIFFRACTIONf_plane_restr0.0051648
X-RAY DIFFRACTIONf_dihedral_angle_d15.3883496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3338-2.39220.38621000.28992947304787
2.3922-2.45680.33822000.271433543554100
2.4568-2.52910.33851000.260634553555100
2.5291-2.61070.36351440.250434223566100
2.6107-2.7040.34561560.241933933549100
2.704-2.81220.34451000.249834823582100
2.8122-2.94020.30992000.245833323532100
2.9402-3.09510.30441000.237134823582100
3.0951-3.2890.29182000.234433883588100
3.289-3.54270.30131000.208835173617100
3.5427-3.89890.25542000.17234073607100
3.8989-4.46240.20381000.142535253625100
4.4624-5.61930.17871000.135235683668100
5.6193-38.18440.17682000.144636263826100

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