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- PDB-8ur1: Crystal structure N-acetylneuraminate lyase (NanA) from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 8ur1
TitleCrystal structure N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound halide free active site)
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
NITRATE ION / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Crystal structure N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound halide free active site)
Authors: Lovell, S. / Liu, L. / Seibold, S. / Mian, M.R.
History
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,99119
Polymers33,7391
Non-polymers1,25318
Water3,117173
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)139,96576
Polymers134,9544
Non-polymers5,01072
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 area20770 Å2
ΔGint-351 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.400, 96.400, 205.596
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-307-

CL

21A-309-

SO4

31A-316-

NO3

41A-316-

NO3

51A-401-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetylneuraminate lyase


Mass: 33738.566 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 , 7 types, 191 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus C11: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4 KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to ...Details: Morpheus C11: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4 KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Cryo: direct. This structure has no halides near KPI 165 in the active which resulted in movement of a nearby loop is the previous structures.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Sep 26, 2023
RadiationMonochromator: HELIOS MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→46.93 Å / Num. obs: 33838 / % possible obs: 100 % / Redundancy: 42.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.036 / Rrim(I) all: 0.232 / Χ2: 0.94 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 30.7 % / Rmerge(I) obs: 1.93 / Num. measured all: 82554 / Num. unique obs: 2690 / CC1/2: 0.789 / Rpim(I) all: 0.354 / Rrim(I) all: 1.963 / Χ2: 0.77 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.93 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1649 4.88 %
Rwork0.1827 --
obs0.1843 33767 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 67 173 2523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092387
X-RAY DIFFRACTIONf_angle_d0.8943227
X-RAY DIFFRACTIONf_dihedral_angle_d15.254869
X-RAY DIFFRACTIONf_chiral_restr0.047361
X-RAY DIFFRACTIONf_plane_restr0.008417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.31151440.2512581X-RAY DIFFRACTION100
2.16-2.230.29131540.23482603X-RAY DIFFRACTION100
2.23-2.310.30181320.21852617X-RAY DIFFRACTION100
2.31-2.40.25191210.20542638X-RAY DIFFRACTION100
2.4-2.510.25381460.19022614X-RAY DIFFRACTION100
2.51-2.650.19021350.17932650X-RAY DIFFRACTION100
2.65-2.810.24951430.1852632X-RAY DIFFRACTION100
2.81-3.030.20241140.18562708X-RAY DIFFRACTION100
3.03-3.330.21281330.17742676X-RAY DIFFRACTION100
3.33-3.820.17931380.16182708X-RAY DIFFRACTION100
3.82-4.810.15121380.14252755X-RAY DIFFRACTION100
4.81-46.930.2281510.20192936X-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)
12.0015-0.1291-0.43980.87310.19441.54560.0117-0.18140.03810.1958-0.0843-0.1149-0.09420.22020.07140.3037-0.0283-0.04950.24790.04020.2318-31.5126-1.064428.4575
21.63780.2439-0.05160.42560.17681.11530.1427-0.1034-0.02050.1847-0.0355-0.0442-0.09950.0159-0.02370.3138-0.01230.00640.1743-0.01490.2416-41.66447.405220.0397
36.97880.74343.2522.7463-0.34895.9803-0.01060.08920.95590.0107-0.1978-0.2486-0.87850.30020.30910.35260.00220.05010.12950.00030.3154-41.36916.46720.1989
41.066-0.4995-0.29570.79120.63622.0220.06890.04780.04930.146-0.1474-0.1184-0.13510.10620.07050.2574-0.0426-0.00430.2030.03520.2658-30.86388.162510.2605
55.33950.5494-3.87083.2738-1.517.83090.0632-0.3138-0.18050.1036-0.2368-0.4827-0.04620.81390.16720.1920.0103-0.05620.29170.09240.3019-17.633-5.747611.8062
63.09443.1925-3.24124.6846-2.52524.504-0.1148-0.019-0.778-0.2255-0.1739-0.52270.51910.25390.26010.29580.0888-0.03250.23850.02230.2752-24.0321-12.74725.9863
73.2776-1.4396-0.06331.2981-0.43911.24640.1106-0.1317-0.25360.1117-0.17940.00580.1370.17820.06830.27610.0107-0.04880.1730.05630.2116-34.6506-16.967422.5315
87.25592.6980.20413.63970.85211.8822-0.08160.057-0.46320.01420.0104-0.06210.45940.44050.04310.3650.1581-0.03570.28540.03310.3037-25.2901-22.439316.4263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 249 )
7X-RAY DIFFRACTION7chain 'A' and (resid 250 through 278 )
8X-RAY DIFFRACTION8chain 'A' and (resid 279 through 296 )

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