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- PDB-8u90: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsi... -

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Basic information

Entry
Database: PDB / ID: 8u90
TitleCrystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, hexagonal form)
ComponentsN-acetylneuraminate lyase
KeywordsLIPID TRANSPORT / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / N-acetylneuraminate lyase
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, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
IODIDE ION / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (Apo, hexagonal form)
Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P.
History
DepositionSep 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,42111
Polymers33,6701
Non-polymers75210
Water4,558253
1
A: N-acetylneuraminate lyase
hetero molecules

A: N-acetylneuraminate lyase
hetero molecules

A: N-acetylneuraminate lyase
hetero molecules

A: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,68444
Polymers134,6784
Non-polymers3,00640
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area15610 Å2
ΔGint-166 kcal/mol
Surface area38670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.599, 97.599, 204.905
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-304-

CL

21A-305-

IOD

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetylneuraminate lyase


Mass: 33669.527 Da / Num. of mol.: 1 / Mutation: V93A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: nanA / Plasmid: KlaeA.01563.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FJT8

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.18 Å3/Da / Density % sol: 70.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus B7: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM HEPES/MOPS, pH 7.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein ...Details: Morpheus B7: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM HEPES/MOPS, pH 7.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Plate 13191 well B7 drop 1. Puck: PSL-1302, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 20, 2023
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→48.8 Å / Num. obs: 50082 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.016 / Rrim(I) all: 0.099 / Χ2: 0.99 / Net I/σ(I): 28.4 / Num. measured all: 1963723
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 99.9 % / Redundancy: 37.9 % / Rmerge(I) obs: 2.685 / Num. measured all: 113941 / Num. unique obs: 3009 / CC1/2: 0.911 / Rpim(I) all: 0.44 / Rrim(I) all: 2.722 / Χ2: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4933: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.94 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.23 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 2474 4.96 %
Rwork0.1707 --
obs0.1721 49869 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 30 253 2565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092414
X-RAY DIFFRACTIONf_angle_d0.9853273
X-RAY DIFFRACTIONf_dihedral_angle_d14.293890
X-RAY DIFFRACTIONf_chiral_restr0.054370
X-RAY DIFFRACTIONf_plane_restr0.01426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.3241300.28922585X-RAY DIFFRACTION100
1.89-1.920.30121330.26732559X-RAY DIFFRACTION99
1.92-1.970.27391140.2342590X-RAY DIFFRACTION99
1.97-2.010.26381260.21752579X-RAY DIFFRACTION99
2.01-2.060.24921490.19712573X-RAY DIFFRACTION100
2.06-2.120.20781320.17642599X-RAY DIFFRACTION100
2.12-2.180.20691410.16682571X-RAY DIFFRACTION99
2.18-2.250.1941250.16642607X-RAY DIFFRACTION100
2.25-2.330.1781520.15452589X-RAY DIFFRACTION100
2.33-2.420.16691440.15312594X-RAY DIFFRACTION100
2.42-2.530.22981150.15782627X-RAY DIFFRACTION100
2.53-2.670.25011330.16432638X-RAY DIFFRACTION100
2.67-2.830.1991540.16412620X-RAY DIFFRACTION100
2.84-3.050.19671360.17082669X-RAY DIFFRACTION100
3.05-3.360.21381340.1762669X-RAY DIFFRACTION100
3.36-3.850.20921520.16022675X-RAY DIFFRACTION100
3.85-4.840.14161420.13612744X-RAY DIFFRACTION100
4.84-35.940.20641620.19662907X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7098-1.02450.03332.1094-0.47162.0159-0.0179-0.13810.14870.2599-0.0291-0.1142-0.07140.22150.06650.335-0.0345-0.04460.23340.00370.2824-34.60822.002326.4838
20.9042-0.144-0.45241.2715-0.41381.44150.04730.0463-0.0365-0.0121-0.0895-0.09890.05260.21090.05350.3114-0.0091-0.05730.32640.0320.2887-29.2207-3.934112.7041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 296 )

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