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- PDB-1ezi: Structure of a sialic acid activating synthetase, CMP acylneurami... -

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Basic information

Entry
Database: PDB / ID: 1ezi
TitleStructure of a sialic acid activating synthetase, CMP acylneuraminate synthetase in the presence and absence of CDP
ComponentsCMP-N-ACETYLNEURAMINIC ACID SYNTHETASE
KeywordsTRANSFERASE / HOMODIMER / ALPHA-BETA-ALPHA
Function / homology
Function and homology information


N-acylneuraminate cytidylyltransferase / N-acylneuraminate cytidylyltransferase activity / cytoplasm
Similarity search - Function
Acylneuraminate cytidylyltransferase / Cytidylyltransferase / : / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMosimann, S.C. / Gilbert, M. / Dombrowski, D. / Wakarchuk, W. / Strynadka, N.C.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure of a sialic acid-activating synthetase, CMP-acylneuraminate synthetase in the presence and absence of CDP.
Authors: Mosimann, S.C. / Gilbert, M. / Dombroswki, D. / To, R. / Wakarchuk, W. / Strynadka, N.C.
History
DepositionMay 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: CMP-N-ACETYLNEURAMINIC ACID SYNTHETASE
B: CMP-N-ACETYLNEURAMINIC ACID SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)50,3102
Polymers50,3102
Non-polymers00
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-24 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.980, 59.520, 157.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CMP-N-ACETYLNEURAMINIC ACID SYNTHETASE / ACYLNEURAMINATE CYTIDYLYLTRANSFERASE


Mass: 25154.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A0Z8, N-acylneuraminate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% PEG 2000, 100 mM Tris-HCl, 1 % Ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.0 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 mMEDTA1drop
616 %PEG20001reservoir
7100 mMTris-HCl1reservoir
810 mM1reservoirMgCl2
91 mMdithiothreitol1reservoir
1010 mMCDP1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. obs: 22325 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3 % / Rmerge(I) obs: 0.22 / % possible all: 83.4
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 25606 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementResolution: 2→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2016621.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5
Details: THE FOLLOWING RESIDUES HAVE BEEN MODELED AS ALA: LYS(A 16), LEU(A 20), GLN(A 205), LEU(A 214), LYS(B 125), GLU(B 213), GLN(B 217), GLN(B 218), ASN(B 221).
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1235 4.9 %RANDOM
Rwork0.212 ---
obs0.212 25030 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.04 Å2 / ksol: 0.3383 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.32 Å20 Å20 Å2
2--6.98 Å20 Å2
3----11.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 0 404 3666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.52.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 171 4.9 %
Rwork0.312 3323 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 1.5 / % reflection Rfree: 5 % / Rfactor Rfree: 0.267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.342 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.312

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