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- PDB-9ftb: Aeromonas caviae CMP-Pse5A7Ac Synthetase -

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Basic information

Entry
Database: PDB / ID: 9ftb
TitleAeromonas caviae CMP-Pse5A7Ac Synthetase
ComponentsNeuA
KeywordsTRANSFERASE / Carbohydrate synthesis / Pseudaminic Acid Synthesis / CMP-Transferase
Function / homologyPseudaminic acid cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / Acylneuraminate cytidylyltransferase / Cytidylyltransferase / : / Nucleotide-diphospho-sugar transferases / NeuA
Function and homology information
Biological speciesAeromonas caviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKeenan, T. / Fascione, M.A. / Cowan, A.R. / Hemsworth, G.R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101044024European Union
CitationJournal: Structure / Year: 2024
Title: Structural dissection of the CMP-pseudaminic acid synthetase, PseF.
Authors: Keenan, T. / Cowan, A.R. / Flack, E.K.P. / Hatton, N.E. / Walklett, A.J. / Thomas, G.H. / Hemsworth, G.R. / Fascione, M.A.
History
DepositionJun 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NeuA


Theoretical massNumber of molelcules
Total (without water)28,0121
Polymers28,0121
Non-polymers00
Water2,396133
1
A: NeuA

A: NeuA


Theoretical massNumber of molelcules
Total (without water)56,0242
Polymers56,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area3380 Å2
ΔGint-26 kcal/mol
Surface area22530 Å2
Unit cell
Length a, b, c (Å)109.527, 109.527, 87.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

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Components

#1: Protein NeuA


Mass: 28011.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas caviae (bacteria) / Gene: neuA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9R9S4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1% w/v Tryptone, 0.05 M HEPES sodium pH 6.5, 14% w/v PEG3350, 0.001 M sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→64.223 Å / Num. obs: 24845 / % possible obs: 100 % / Redundancy: 40 % / CC1/2: 0.999 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.048 / Rrim(I) all: 0.223 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.11-64.1431.90.1222910.9970.0270.125
1.9-1.9441.84.34615700.9170.9434.447

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→64.223 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.202 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2406 1187 4.786 %
Rwork0.1916 23616 -
all0.194 --
obs-24803 99.984 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.476 Å20.238 Å20 Å2
2--0.476 Å2-0 Å2
3----1.544 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 0 133 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0121912
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161771
X-RAY DIFFRACTIONr_angle_refined_deg2.1741.652615
X-RAY DIFFRACTIONr_angle_other_deg0.7171.5764073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.83511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51310298
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.791089
X-RAY DIFFRACTIONr_chiral_restr0.1080.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
X-RAY DIFFRACTIONr_nbd_refined0.2260.2363
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.21557
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2946
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.080.25
X-RAY DIFFRACTIONr_nbd_other0.1830.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.216
X-RAY DIFFRACTIONr_mcbond_it3.0082.095948
X-RAY DIFFRACTIONr_mcbond_other3.0082.095948
X-RAY DIFFRACTIONr_mcangle_it4.1243.7461187
X-RAY DIFFRACTIONr_mcangle_other4.1233.7471188
X-RAY DIFFRACTIONr_scbond_it4.0372.403964
X-RAY DIFFRACTIONr_scbond_other4.0352.404965
X-RAY DIFFRACTIONr_scangle_it5.8244.2251424
X-RAY DIFFRACTIONr_scangle_other5.8224.2261425
X-RAY DIFFRACTIONr_lrange_it7.73321.182146
X-RAY DIFFRACTIONr_lrange_other7.7120.7562126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.367920.33416960.33617880.8860.9081000.307
1.949-2.0030.283840.25416560.25517400.9410.9521000.232
2.003-2.0610.297820.22916350.23217170.9270.9631000.203
2.061-2.1240.303780.22615820.22916600.9420.9641000.197
2.124-2.1940.269830.21815290.2216120.9470.9671000.19
2.194-2.2710.308690.26314770.26515460.9390.9491000.225
2.271-2.3560.273780.20314310.20615090.9540.9721000.178
2.356-2.4520.252740.18713830.1914570.9650.9791000.16
2.452-2.5610.26660.16513320.1713980.9620.9831000.144
2.561-2.6860.224380.17812950.1813330.9610.9791000.155
2.686-2.8310.275730.18612080.19212810.9520.9771000.166
2.831-3.0020.254560.18511570.18812130.9540.9791000.171
3.002-3.2090.221680.18410850.18611530.970.9791000.173
3.209-3.4660.229520.210110.20210630.9730.9781000.195
3.466-3.7950.214420.1839640.18510080.9710.98299.80160.18
3.795-4.2410.208390.1568600.1588990.9780.9861000.162
4.241-4.8940.198410.1387720.148130.9810.991000.151
4.894-5.9850.178300.1766710.1767010.9820.9851000.19
5.985-8.4280.264260.25380.2035640.9630.9781000.216
8.428-64.2230.19160.2133350.2123520.980.96799.71590.245
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)
15.41361.25350.47681.58-1.37725.4838-0.06690.1943-0.2014-0.1174-0.0842-0.1414-0.14620.54110.15110.1041-0.05570.00050.1565-0.00240.0179-6.873-31.7739.508
20.24090.4290.72970.97161.74899.3481-0.023-0.07130.0899-0.1675-0.17660.1744-0.1592-0.65730.19960.10440.0148-0.01890.1249-0.01270.0388-24.685-39.43-6.015
318.57483.2852-7.3640.5921-1.10667.1584-0.58371.12870.2347-0.10640.26230.0668-0.32980.74760.32140.4072-0.0802-0.03020.53660.09620.0976-10.834-26.398-8.644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA13 - 141
2X-RAY DIFFRACTION2ALLA142 - 220
3X-RAY DIFFRACTION3ALLA221 - 246

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