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

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Basic information

Entry
Database: PDB / ID: 5kze
TitleN-acetylneuraminate lyase from methicillin-resistant Staphylococcus aureus
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / TIM-barrel / N-acetylneuraminate lyase
Function / homology
Function and homology information


N-acetylneuraminate lyase / N-acetylneuraminate lyase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytoplasm / 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
N-acetylneuraminate lyase / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
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

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
E: N-acetylneuraminate lyase
F: N-acetylneuraminate lyase
G: N-acetylneuraminate lyase
H: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,11724
Polymers264,6128
Non-polymers1,50516
Water35,6341978
1
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
F: N-acetylneuraminate lyase
H: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,05812
Polymers132,3064
Non-polymers7538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-134 kcal/mol
Surface area40290 Å2
MethodPISA
2
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
E: N-acetylneuraminate lyase
G: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,05812
Polymers132,3064
Non-polymers7538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-133 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.110, 130.540, 108.520
Angle α, β, γ (deg.)90.000, 90.010, 90.000
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: 33076.465 Da / Num. of mol.: 8
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1978 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, ammonium sulfate, Bis Tris

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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: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.41
ReflectionResolution: 1.74→32.223 Å / Num. obs: 213902 / % possible obs: 94 % / Redundancy: 3.6 % / Rsym value: 0.056 / Net I/av σ(I): 11.734 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.74-1.833.20.2962.6188.6
1.83-1.953.30.1993.8192.9
1.95-2.083.40.1365.7194.6
2.08-2.253.60.0978195.4
2.25-2.463.70.07610.1195.8
2.46-2.753.80.06212.3195.9
2.75-3.183.90.04615.9196
3.18-3.893.90.03520195.9
3.89-5.53.90.0322.5195.4
5.5-32.2233.80.0317.8192.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f6p

1f6p


Resolution: 1.74→32.223 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.16
RfactorNum. reflection% reflection
Rfree0.2031 2008 94 %
Rwork0.1415 --
obs0.1444 213902 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.21 Å2 / Biso mean: 15.0893 Å2 / Biso min: 7.38 Å2
Refinement stepCycle: final / Resolution: 1.74→32.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18608 0 152 1978 20738
Biso mean--23.03 19.92 -
Num. residues----2336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619024
X-RAY DIFFRACTIONf_angle_d0.9625712
X-RAY DIFFRACTIONf_chiral_restr0.0382848
X-RAY DIFFRACTIONf_plane_restr0.0043368
X-RAY DIFFRACTIONf_dihedral_angle_d13.9717096
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 (%)
1.7547-1.79750.2941820.2138135351371788
1.7975-1.84480.2168940.2059139971409190
1.8448-1.89760.2561840.1882141591434391
1.8976-1.95690.2311940.1763143031439793
1.9569-2.02450.2257980.1683144681456694
2.0245-2.10240.19661900.1604145381472894
2.1024-2.1940.2072980.1585145941469295
2.194-2.30390.2007970.1521146711476895
2.3039-2.43980.20671900.1464146901488095
2.4398-2.61470.1989960.1422147101480695
2.6147-2.85380.2289930.1408148191491295
2.8538-3.21440.20281940.1324146791487395
3.2144-3.87440.1681970.1206147741487195
3.8744-6.15960.17671860.1074147051489194

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