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- PDB-5zjm: Crystal structure of N-acetylneuraminate lyase from Fusobacterium... -

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Basic information

Entry
Database: PDB / ID: 5zjm
TitleCrystal structure of N-acetylneuraminate lyase from Fusobacterium nucleatum
ComponentsN-acetylneuraminate lyase
KeywordsLYASE / N-acetylneuraminate lyase / Sialic acid catabolism / TIM-barrel
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 class I / Aldolase-type TIM barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-acetylneuraminate lyase
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.323 Å
AuthorsKumar, J.P. / Rao, H. / Nayak, V. / Subramanian, R.
Funding support India, 4items
OrganizationGrant numberCountry
BT/IN/SWEDEN/41/SR/2013 India
BT/PR5081/INF/156/2012 India
BT/PR12422/MED/31/287/214 India
BT/INF/22/SP22660/2017 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures and kinetics of N-acetylneuraminate lyase from Fusobacterium nucleatum
Authors: Kumar, J.P. / Rao, H. / Nayak, V. / Ramaswamy, S.
History
DepositionMar 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9187
Polymers131,7324
Non-polymers1863
Water25214
1
A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
hetero molecules

A: N-acetylneuraminate lyase
B: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9818
Polymers131,7324
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9900 Å2
ΔGint-43 kcal/mol
Surface area42540 Å2
MethodPISA
2
C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
hetero molecules

C: N-acetylneuraminate lyase
D: N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,8566
Polymers131,7324
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9300 Å2
ΔGint-51 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.165, 108.977, 141.137
Angle α, β, γ (deg.)90.000, 96.880, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 0 and (name N or name...
21(chain B and ((resid 0 and (name N or name...
31(chain C and ((resid 0 and (name N or name...
41(chain D and (resid 0 or (resid 1 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHE(chain A and ((resid 0 and (name N or name...AA02
12PHEPHELYSLYS(chain A and ((resid 0 and (name N or name...AA0 - 2892 - 291
13PHEPHELYSLYS(chain A and ((resid 0 and (name N or name...AA0 - 2892 - 291
14PHEPHELYSLYS(chain A and ((resid 0 and (name N or name...AA0 - 2892 - 291
15PHEPHELYSLYS(chain A and ((resid 0 and (name N or name...AA0 - 2892 - 291
21PHEPHEPHEPHE(chain B and ((resid 0 and (name N or name...BB02
22GLYGLYLYSLYS(chain B and ((resid 0 and (name N or name...BB-1 - 2891 - 291
23GLYGLYLYSLYS(chain B and ((resid 0 and (name N or name...BB-1 - 2891 - 291
24GLYGLYLYSLYS(chain B and ((resid 0 and (name N or name...BB-1 - 2891 - 291
25GLYGLYLYSLYS(chain B and ((resid 0 and (name N or name...BB-1 - 2891 - 291
31PHEPHEPHEPHE(chain C and ((resid 0 and (name N or name...CC02
32PHEPHELYSLYS(chain C and ((resid 0 and (name N or name...CC0 - 2892 - 291
33PHEPHELYSLYS(chain C and ((resid 0 and (name N or name...CC0 - 2892 - 291
34PHEPHELYSLYS(chain C and ((resid 0 and (name N or name...CC0 - 2892 - 291
35PHEPHELYSLYS(chain C and ((resid 0 and (name N or name...CC0 - 2892 - 291
41PHEPHEPHEPHE(chain D and (resid 0 or (resid 1 and (name...DD02
42METMETMETMET(chain D and (resid 0 or (resid 1 and (name...DD13
43GLYGLYLYSLYS(chain D and (resid 0 or (resid 1 and (name...DD-1 - 2891 - 291
44GLYGLYLYSLYS(chain D and (resid 0 or (resid 1 and (name...DD-1 - 2891 - 291
45GLYGLYLYSLYS(chain D and (resid 0 or (resid 1 and (name...DD-1 - 2891 - 291
46GLYGLYLYSLYS(chain D and (resid 0 or (resid 1 and (name...DD-1 - 2891 - 291
47GLYGLYLYSLYS(chain D and (resid 0 or (resid 1 and (name...DD-1 - 2891 - 291
48GLYGLYLYSLYS(chain D and (resid 0 or (resid 1 and (name...DD-1 - 2891 - 291

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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: 32933.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / Gene: nanA / Plasmid: pMK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RDN6, N-acetylneuraminate lyase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1M CHES, pH 9.5 , 10%(w/v) PEG 3000 and 5mM ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978875 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978875 Å / Relative weight: 1
ReflectionResolution: 2.32→49.24 Å / Num. obs: 64567 / % possible obs: 94.9 % / Redundancy: 2.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.032 / Rrim(I) all: 0.051 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1 / % possible all: 94.3

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.32-2.382.30.46643040.8760.3710.6
10.9-49.242.40.0256500.9980.0190.031

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IMC

4imc


Resolution: 2.323→47.108 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.28
RfactorNum. reflection% reflection
Rfree0.2451 3195 4.96 %
Rwork0.2023 --
obs0.2044 64385 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.91 Å2 / Biso mean: 68.7699 Å2 / Biso min: 36.34 Å2
Refinement stepCycle: final / Resolution: 2.323→47.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8881 0 12 14 8907
Biso mean--85.64 60.66 -
Num. residues----1162
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3216X-RAY DIFFRACTION4.026TORSIONAL
12B3216X-RAY DIFFRACTION4.026TORSIONAL
13C3216X-RAY DIFFRACTION4.026TORSIONAL
14D3216X-RAY DIFFRACTION4.026TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3231-2.35780.45731410.43832602274393
2.3578-2.39470.45471370.40262632276995
2.3947-2.43390.43471570.37252634279194
2.4339-2.47590.3731550.35822610276594
2.4759-2.52090.42311140.36632624273892
2.5209-2.56940.35991180.33672602272093
2.5694-2.62180.35681390.31682629276893
2.6218-2.67880.36491200.30512642276294
2.6788-2.74110.31541450.28692642278795
2.7411-2.80970.29691440.24952728287295
2.8097-2.88560.26821580.25162647280596
2.8856-2.97050.31471180.23732737285597
2.9705-3.06640.32051200.22912774289498
3.0664-3.1760.26591480.21832720286896
3.176-3.30310.27641520.22182702285496
3.3031-3.45340.26091470.21732688283596
3.4534-3.63540.25281400.19912659279995
3.6354-3.86310.21821350.18142631276694
3.8631-4.16120.23031370.16812662279994
4.1612-4.57960.17441360.14522661279794
4.5796-5.24160.18731460.14682633277993
5.2416-6.60090.19821520.19162622277493
6.6009-47.11740.20211360.15772709284593
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)
12.50290.1630.15995.2776-1.19391.60510.0083-0.069-0.033-0.15430.16690.78630.1604-0.3154-0.14930.4536-0.06380.04790.72160.01920.573-29.0662-3.430217.2148
22.87150.26880.523.4157-0.81291.7342-0.09080.24180.2194-0.157-0.0260.008-0.09690.04170.04420.5085-0.04830.00220.6519-0.03930.5006-14.2189.264615.3577
32.6220.6255-0.24564.41640.7951.54550.1767-0.1725-0.21430.2340.0346-0.13540.0481-0.1434-0.04180.4537-0.0845-0.02810.65350.07720.4308-13.7305-16.004321.2347
42.79980.5208-0.39862.6282-0.31991.9187-0.0127-0.10640.2748-0.06120.1146-0.1881-0.26980.2566-0.12610.5529-0.1-0.14440.8116-0.01230.603826.91167.519718.5769
52.3367-0.06330.08093.92651.38521.49510.0937-0.2546-0.12750.29270.1041-0.67890.10770.7984-0.11560.4762-0.0279-0.08350.7294-0.06810.659432.2241-2.630314.7652
62.68280.2898-1.42051.48270.83051.8765-0.13010.3427-0.1484-0.22550.0547-0.23360.1029-0.07360.00160.5278-0.0693-0.0890.7110.02650.512515.3064-11.393713.6111
71.40910.5182-0.37342.2569-0.54231.19180.1524-0.10160.1160.0592-0.0181-0.06360.02340.1218-0.08530.4754-0.1053-0.06280.7055-0.03160.507913.1913.193821.671
82.8659-1.02060.64725.08340.56031.9011-0.02430.0547-0.2301-0.0710.218-0.4719-0.046-0.0017-0.17260.44550.07270.05490.5023-0.05280.47418.050935.089551.3839
93.5494-0.41020.52626.34321.36681.9473-0.07340.3341-0.13140.05520.1862-1.41920.13920.8672-0.13930.47910.01-0.01930.6265-0.05850.755123.795945.284354.8969
103.0949-0.17730.66553.99451.06162.0167-0.1155-0.31160.23140.1190.0105-0.0243-0.1816-0.13070.13230.4330.0621-0.01790.43610.00110.41975.862752.339854.9332
112.7214-0.28450.22854.9961-0.2181.76240.19730.3011-0.2455-0.1469-0.07690.0724-0.02360.2621-0.10120.38550.0794-0.01370.4373-0.07960.38145.347927.046748.7941
124.8211-3.7427-3.11344.89242.764.77980.2927-0.05920.0496-0.54520.08450.2955-0.6857-0.3147-0.21350.50920.1004-0.11790.45990.00640.4635-35.324850.634753.4344
132.3510.2691-0.36324.6536-1.60622.0134-0.05280.0558-0.12630.0850.09680.4585-0.0229-0.0617-0.16950.38230.0222-0.1430.46140.02470.4938-38.305445.023653.1443
142.46760.378-1.36372.2129-1.3131.6712-0.064-0.2787-0.29040.22310.0209-0.03750.13040.1640.02730.54270.048-0.12590.4492-0.01950.4854-22.851533.207954.9695
152.2954-0.4237-0.83942.48650.36311.69290.08440.18090.1853-0.065-0.1082-0.07360.0769-0.1252-0.04130.38270.0574-0.10050.41580.00740.411-22.386758.632648.8786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 95 )A0 - 95
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 204 )A96 - 204
3X-RAY DIFFRACTION3chain 'A' and (resid 205 through 289 )A205 - 289
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 52 )B-1 - 52
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 95 )B53 - 95
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 186 )B96 - 186
7X-RAY DIFFRACTION7chain 'B' and (resid 187 through 289 )B187 - 289
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 52 )C0 - 52
9X-RAY DIFFRACTION9chain 'C' and (resid 53 through 95 )C53 - 95
10X-RAY DIFFRACTION10chain 'C' and (resid 96 through 204 )C96 - 204
11X-RAY DIFFRACTION11chain 'C' and (resid 205 through 289 )C205 - 289
12X-RAY DIFFRACTION12chain 'D' and (resid -1 through 19 )D-1 - 19
13X-RAY DIFFRACTION13chain 'D' and (resid 20 through 95 )D20 - 95
14X-RAY DIFFRACTION14chain 'D' and (resid 96 through 204 )D96 - 204
15X-RAY DIFFRACTION15chain 'D' and (resid 205 through 289 )D205 - 289

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