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- PDB-8u93: Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsi... -

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Basic information

Entry
Database: PDB / ID: 8u93
TitleCrystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (PEG bound)
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
Chem-1PG / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / DI(HYDROXYETHYL)ETHER / N-acetylneuraminate lyase
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 (PEG bound)
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
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)34,6148
Polymers33,7391
Non-polymers8757
Water2,720151
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)138,45432
Polymers134,9544
Non-polymers3,50028
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 area15130 Å2
ΔGint-34 kcal/mol
Surface area40370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.406, 96.406, 205.982
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-302-

CL

21A-501-

HOH

31A-510-

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 , 6 types, 158 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 4.1 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Index E8: 35% v/v Pentaerythritol propoxylate (5/4 PO/OH), 0.05 M HEPES pH 7.5, 0.2 M Potassium chloride. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to ...Details: Index E8: 35% v/v Pentaerythritol propoxylate (5/4 PO/OH), 0.05 M HEPES pH 7.5, 0.2 M Potassium chloride. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Plate 13192, well E8 drop 2. Puck: PSL-1406, 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: 1.9→48.2 Å / Num. obs: 45341 / % possible obs: 99.8 % / Redundancy: 39.6 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.012 / Rrim(I) all: 0.076 / Χ2: 0.97 / Net I/σ(I): 30.8 / Num. measured all: 1794646
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.4 % / Redundancy: 41.5 % / Rmerge(I) obs: 3.276 / Num. measured all: 118584 / Num. unique obs: 2859 / CC1/2: 0.914 / Rpim(I) all: 0.508 / Rrim(I) all: 3.315 / Χ2: 0.93 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5057: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.94 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 2288 5.07 %
Rwork0.1832 --
obs0.1842 45146 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 52 151 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092390
X-RAY DIFFRACTIONf_angle_d1.0933224
X-RAY DIFFRACTIONf_dihedral_angle_d15.808886
X-RAY DIFFRACTIONf_chiral_restr0.055364
X-RAY DIFFRACTIONf_plane_restr0.011416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.38581180.32262623X-RAY DIFFRACTION99
1.94-1.990.30591250.27082607X-RAY DIFFRACTION99
1.99-2.040.24061360.23782611X-RAY DIFFRACTION99
2.04-2.090.25531450.20672626X-RAY DIFFRACTION99
2.09-2.150.18971350.19732601X-RAY DIFFRACTION99
2.15-2.220.23491400.19012636X-RAY DIFFRACTION99
2.22-2.30.21231320.18772661X-RAY DIFFRACTION99
2.3-2.390.21091290.18512654X-RAY DIFFRACTION99
2.39-2.50.2071430.19822642X-RAY DIFFRACTION99
2.5-2.630.22031610.19372643X-RAY DIFFRACTION100
2.63-2.80.23511570.19522670X-RAY DIFFRACTION100
2.8-3.020.20361630.1992687X-RAY DIFFRACTION100
3.02-3.320.27241490.21512715X-RAY DIFFRACTION100
3.32-3.80.17591320.18392746X-RAY DIFFRACTION100
3.8-4.780.15541700.14362764X-RAY DIFFRACTION100
4.79-36.940.20091530.17112972X-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)
11.8705-1.1212-0.13522.3796-0.68872.1579-0.0563-0.18610.11130.362-0.004-0.0201-0.13760.20490.0730.4649-0.0323-0.06310.3009-0.00160.3416-34.11392.264126.4972
20.9316-1.2096-1.48022.45131.91154.51850.13130.23190.08020.0963-0.19740.0903-0.2714-0.33340.06420.4115-0.0506-0.02630.4250.05470.3986-31.06478.351110.1603
31.88920.3492-1.19711.554-1.00222.6486-0.0517-0.0799-0.2254-0.0314-0.1425-0.12980.35150.43620.22910.42540.0749-0.050.36580.05090.377-26.3287-14.584314.9864
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 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 296 )

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