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- PDB-3ewi: Structural analysis of the C-terminal domain of murine CMP-Sialic... -

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Basic information

Entry
Database: PDB / ID: 3ewi
TitleStructural analysis of the C-terminal domain of murine CMP-Sialic acid Synthetase
ComponentsN-acylneuraminate cytidylyltransferase
KeywordsTRANSFERASE / beta barrel / HAD-like / rossmannoid fold / Nucleotidyltransferase / Nucleus
Function / homology
Function and homology information


CMP-N-acetylneuraminate biosynthetic process / N-acylneuraminate cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / Sialic acid metabolism / N-acetylneuraminate metabolic process / nucleus
Similarity search - Function
Acylneuraminate cytidylyltransferase / Cytidylyltransferase / HAD superfamily/HAD-like / Nucleotide-diphospho-sugar transferases / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesMus Musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsOschlies, M. / Dickmanns, A. / Stummeyer, K. / Gerardy-Schahn, R. / Ficner, R. / Muenster-Kuehnel, A.K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: A C-terminal phosphatase module conserved in vertebrate CMP-sialic acid synthetases provides a tetramerization interface for the physiologically active enzyme.
Authors: Oschlies, M. / Dickmanns, A. / Haselhorst, T. / Schaper, W. / Stummeyer, K. / Tiralongo, J. / Weinhold, B. / Gerardy-Schahn, R. / von Itzstein, M. / Ficner, R. / Munster-Kuhnel, A.K.
History
DepositionOct 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylneuraminate cytidylyltransferase
B: N-acylneuraminate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)36,7452
Polymers36,7452
Non-polymers00
Water3,261181
1
A: N-acylneuraminate cytidylyltransferase
B: N-acylneuraminate cytidylyltransferase

A: N-acylneuraminate cytidylyltransferase
B: N-acylneuraminate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)73,4894
Polymers73,4894
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6060 Å2
ΔGint-29 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.090, 37.490, 78.830
Angle α, β, γ (deg.)90.00, 116.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6 / Auth seq-ID: 7 - 163 / Label seq-ID: 7 - 163

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein N-acylneuraminate cytidylyltransferase / / CMP-N-acetylneuraminic acid synthetase / CMP-NeuNAc synthetase


Mass: 18372.297 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus Musculus (house mouse) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q99KK2, N-acylneuraminate cytidylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1843.47
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop8EtOH, Tris, DTT, Neu5Ac, pH 8, vapor diffusion, sitting drop, temperature 277K
2772vapor diffusion, sitting drop7.5EtOH, Tris, DTT, Neu5Ac, pH 7.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.9184
SYNCHROTRONBESSY 14.120.9797, 0.9799, 0.9117
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJun 14, 2007
MARMOSAIC 225 mm CCD2CCDAug 1, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si 111 ChannelSINGLE WAVELENGTHMx-ray1
2Double crystal Si 111 ChannelMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97971
30.97991
40.91171
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 27.64 / Number: 98810 / Rmerge(I) obs: 0.036 / Χ2: 1.01 / D res high: 1.9 Å / Num. obs: 48469 / % possible obs: 98.3
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Chi squaredRedundancyRmerge(I) obs
20500.9944.4
102025683.90.9974.50.017
610120497.91.0034.60.017
561127981.0214.60.019
452510981.0224.60.019
34707797.51.0154.50.024
2.83279197.91.0244.20.038
2.52.8609698.21.0273.80.05
2.32.56125991.0263.20.069
2.22.3385198.40.9912.70.097
22.21042899.10.134
1.92700498.80.245
ReflectionResolution: 1.9→27.43 Å / Num. obs: 24430 / % possible obs: 95.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Χ2: 1.012 / Net I/σ(I): 27.636
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1769 / Rsym value: 0.252 / Χ2: 0.991 / % possible all: 69.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementResolution: 1.9→27.43 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.363 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1256 5.1 %RANDOM
Rwork0.206 ---
obs0.209 24429 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.6 Å2 / Biso mean: 24.153 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.62 Å2
2---0.53 Å20 Å2
3---1.05 Å2
Refine analyzeLuzzati sigma a obs: 0.357 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 0 181 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222430
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9783280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6765325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9825.15895
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78915459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4991513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021769
X-RAY DIFFRACTIONr_nbd_refined0.2070.21305
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.219
Refine LS restraints NCSNumber: 1131 / Type: LOOSE POSITIONAL / Rms dev position: 0.93 Å / Weight position: 5
LS refinement shellResolution: 1.9→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 62 -
Rwork0.271 1112 -
all-1174 -
obs--62.92 %

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