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- PDB-5c54: Crystal structure of a novel N-acetylneuraminic acid lyase from C... -

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Basic information

Entry
Database: PDB / ID: 5c54
TitleCrystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum
ComponentsDihydrodipicolinate synthase/N-acetylneuraminate lyase
KeywordsLYASE / N-acetylneuraminic acid lyase / Aldolase / TIM barrel
Function / homology
Function and homology information


N-acetylneuraminate lyase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
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
Dihydrodipicolinate synthase/N-acetylneuraminate lyase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.601 Å
AuthorsShen, Y. / Zhou, J. / Xie, J.
CitationJournal: To Be Published
Title: Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum
Authors: Shen, Y. / Zhou, J. / Xie, J.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
B: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
C: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
D: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
E: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
F: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
G: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
H: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,99318
Polymers262,0728
Non-polymers92110
Water53,6492978
1
A: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
B: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
C: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
D: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,58910
Polymers131,0364
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-37 kcal/mol
Surface area40330 Å2
MethodPISA
2
E: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
F: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
G: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
H: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,4058
Polymers131,0364
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12110 Å2
ΔGint-36 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.506, 96.285, 163.288
Angle α, β, γ (deg.)90.000, 92.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydrodipicolinate synthase/N-acetylneuraminate lyase


Mass: 32759.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / Gene: Cgl2646 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NMD2, N-acetylneuraminate lyase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2978 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Tris, 1.2 M Lithium chloride, 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97908, 0.96406, 0.97929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.964061
30.979291
ReflectionRedundancy: 7.6 % / Number: 1475197 / Rmerge(I) obs: 0.14 / Χ2: 1.73 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 194501 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.165010.0654.8767.6
4.095.1610.0783.1367.4
3.584.0910.0933.3377.4
3.253.5810.1063.1447.5
3.023.2510.122.5997.6
2.843.0210.1372.0717.6
2.72.8410.1541.7257.6
2.582.710.1791.4847.6
2.482.5810.1991.3477.6
2.392.4810.2351.2537.6
2.322.3910.2581.1927.6
2.252.3210.2871.1367.6
2.192.2510.3331.0777.6
2.142.1910.3631.0257.6
2.092.1410.420.9787.6
2.052.0910.4820.9237.6
2.012.0510.5680.8717.6
1.972.0110.6780.8357.6
1.931.9710.8190.8037.6
1.91.9310.9890.7797.6
ReflectionResolution: 1.6→50 Å / Num. obs: 319011 / % possible obs: 97.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 15.43 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.034 / Rrim(I) all: 0.094 / Χ2: 1.093 / Net I/av σ(I): 20.795 / Net I/σ(I): 11.2 / Num. measured all: 2416688
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.667.50.634312900.8550.2470.681.2696.2
1.66-1.727.60.48313400.910.1860.5151.28196.5
1.72-1.87.60.364315040.9450.1410.3911.21896.8
1.8-1.97.60.257316580.9730.10.2761.1497.1
1.9-2.027.70.182317770.9850.070.1951.16997.5
2.02-2.177.70.129318800.9910.050.1381.10497.9
2.17-2.397.70.102320360.9940.040.111.02698.2
2.39-2.747.60.083322070.9960.0320.0890.92198.6
2.74-3.457.50.064324570.9970.0250.0690.9399.1
3.45-507.30.048328620.9980.0190.0520.89599.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.8.3_1479)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.601→34.268 Å / FOM work R set: 0.8776 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 16084 5.04 %
Rwork0.1633 302867 -
obs0.1648 318951 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.03 Å2 / Biso mean: 19.12 Å2 / Biso min: 6.22 Å2
Refinement stepCycle: final / Resolution: 1.601→34.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18295 0 60 2978 21333
Biso mean--30.42 28.24 -
Num. residues----2473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618857
X-RAY DIFFRACTIONf_angle_d0.99725699
X-RAY DIFFRACTIONf_chiral_restr0.0413086
X-RAY DIFFRACTIONf_plane_restr0.0053332
X-RAY DIFFRACTIONf_dihedral_angle_d12.3246653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6008-1.6190.26955120.220594931000592
1.619-1.63810.25754910.217599391043096
1.6381-1.6580.25055520.214599331048596
1.658-1.6790.25124930.206799351042896
1.679-1.70110.25655210.205399271044896
1.7011-1.72440.2325340.196599911052597
1.7244-1.74910.22455030.1937100241052797
1.7491-1.77520.23875500.190499161046697
1.7752-1.80290.23125110.191100141052597
1.8029-1.83250.24745280.1887100491057797
1.8325-1.8640.21345700.183699681053897
1.864-1.89790.21464880.1774101051059397
1.8979-1.93440.22455440.1844100571060198
1.9344-1.97390.23585570.1816100051056297
1.9739-2.01680.20785230.1731101221064598
2.0168-2.06370.20925100.1694101341064498
2.0637-2.11540.20065470.1672100511059898
2.1154-2.17250.20375210.1704101361065798
2.1725-2.23650.19975800.1668101371071798
2.2365-2.30860.21384980.1647101611065998
2.3086-2.39110.1935190.1669101711069098
2.3911-2.48680.19925730.1722101481072199
2.4868-2.60.21435540.1682102531080799
2.6-2.7370.21285530.1684101701072399
2.737-2.90840.19725770.1698102311080899
2.9084-3.13280.1975780.1671102561083499
3.1328-3.44780.18015520.1579102981085099
3.4478-3.94610.1495440.1357103601090499
3.9461-4.96920.13495530.1199103891094299
4.9692-34.27590.15585480.137104941104299

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