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- PDB-9ftc: Aeromonas caviae CMP-Pse5Ac7Ac synthetase in the presence of CMP-... -

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Basic information

Entry
Database: PDB / ID: 9ftc
TitleAeromonas caviae CMP-Pse5Ac7Ac synthetase in the presence of CMP-Pse5Ac7Ac.
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: 1.5 Å
AuthorsCowan, A.R. / Hemsworth, G.R. / Keenan, T. / Fascione, M.A.
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

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Assembly

Deposited unit
A: NeuA
B: NeuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3034
Polymers56,0242
Non-polymers1,2792
Water7,494416
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-26 kcal/mol
Surface area20370 Å2
Unit cell
Length a, b, c (Å)42.574, 79.007, 74.039
Angle α, β, γ (deg.)90.000, 92.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NeuA


Mass: 28011.840 Da / Num. of mol.: 2
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: Chemical ChemComp-A1IF6 / (2~{R},4~{S},5~{S},6~{S})-5-acetamido-6-[(1~{S},2~{S})-1-acetamido-2-oxidanyl-propyl]-2-[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxane-2-carboxylic acid


Mass: 639.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H34N5O15P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium Nitrate; 0.1 M Bis-Tris Propane pH 6.5; 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→54 Å / Num. obs: 78069 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.037 / Rrim(I) all: 0.054 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.22-543.30.0315000.9860.0310.044
1.5-1.533.50.10638670.9750.10.146

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.571 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.037 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1854 4148 5.315 %
Rwork0.1668 73894 -
all0.168 --
obs-78042 99.65 %
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: 15.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.012 Å2-0 Å2-0.16 Å2
2--0.814 Å20 Å2
3----0.809 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 86 416 4098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163505
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.6665193
X-RAY DIFFRACTIONr_angle_other_deg0.571.5858046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.154525
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.94912.58
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30710580
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.79510173
X-RAY DIFFRACTIONr_chiral_restr0.0860.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
X-RAY DIFFRACTIONr_nbd_refined0.2240.2712
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.23237
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21903
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.218
X-RAY DIFFRACTIONr_nbd_other0.2610.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3780.225
X-RAY DIFFRACTIONr_mcbond_it1.7561.4931828
X-RAY DIFFRACTIONr_mcbond_other1.751.4931828
X-RAY DIFFRACTIONr_mcangle_it2.62.6712279
X-RAY DIFFRACTIONr_mcangle_other2.62.6722280
X-RAY DIFFRACTIONr_scbond_it2.6811.7391972
X-RAY DIFFRACTIONr_scbond_other2.681.7391973
X-RAY DIFFRACTIONr_scangle_it4.0893.0572912
X-RAY DIFFRACTIONr_scangle_other4.0883.0562913
X-RAY DIFFRACTIONr_lrange_it6.1119.0814326
X-RAY DIFFRACTIONr_lrange_other5.92717.3074245
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
1.5-1.5390.1812870.18153840.18157560.9790.98198.52330.176
1.539-1.5810.2153200.16952880.17256690.9740.98398.9240.165
1.581-1.6270.212740.17151080.17354150.9750.98299.39060.168
1.627-1.6770.1942460.16750520.16853270.9760.98399.45560.165
1.677-1.7320.1812710.16248480.16351370.9820.98499.64960.161
1.732-1.7920.2012660.16847240.1750050.9740.98399.70030.168
1.792-1.860.1982850.16645300.16848230.9730.98399.83410.17
1.86-1.9360.1982240.16844050.1746350.9760.98399.87060.174
1.936-2.0220.1961980.17142160.17244180.9780.98399.90950.179
2.022-2.120.22190.17840360.17942550.9750.9821000.188
2.12-2.2340.2072290.16738100.16940390.9760.9831000.18
2.234-2.370.1652270.16135850.16238140.9820.98499.94760.177
2.37-2.5330.191940.1633940.16135910.9770.98499.91650.178
2.533-2.7350.1861820.1631770.16133600.9790.98499.97020.183
2.735-2.9950.2181670.16829260.1730930.9750.9821000.194
2.995-3.3460.21620.18126460.18228080.9750.981000.211
3.346-3.860.1741110.15923660.15924780.9840.98699.95960.192
3.86-4.7170.1371460.13719640.13721110.990.9999.95260.175
4.717-6.6310.1591050.18115210.1816270.9870.98699.93850.23
6.631-42.5710.181350.2039130.2029530.9820.97699.47530.248

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