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- PDB-1qwj: The Crystal Structure of Murine CMP-5-N-Acetylneuraminic Acid Syn... -

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Basic information

Entry
Database: PDB / ID: 1qwj
TitleThe Crystal Structure of Murine CMP-5-N-Acetylneuraminic Acid Synthetase
Componentscytidine monophospho-N-acetylneuraminic acid synthetase
KeywordsTRANSFERASE / CMP-5-N-acetylneuraminic acid synthetase / CMP-Neu5Ac / sialic acid / glycosylation / lipopolysaccharide biosynthesis / sugar-activating enzyme
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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / HAD superfamily / HAD-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-NCC / N-acylneuraminate cytidylyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsKrapp, S. / Muenster-Kuehnel, A.K. / Kaiser, J.T. / Huber, R. / Tiralongo, J. / Gerardy-Schahn, R. / Jacob, U.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure of Murine CMP-5-N-acetylneuraminic Acid Synthetase
Authors: Krapp, S. / Muenster-Kuehnel, A.K. / Kaiser, J.T. / Huber, R. / Tiralongo, J. / Gerardy-Schahn, R. / Jacob, U.
History
DepositionSep 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cytidine monophospho-N-acetylneuraminic acid synthetase
B: cytidine monophospho-N-acetylneuraminic acid synthetase
C: cytidine monophospho-N-acetylneuraminic acid synthetase
D: cytidine monophospho-N-acetylneuraminic acid synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1937
Polymers104,3504
Non-polymers1,8433
Water2,792155
1
A: cytidine monophospho-N-acetylneuraminic acid synthetase
B: cytidine monophospho-N-acetylneuraminic acid synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7893
Polymers52,1752
Non-polymers6141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-11 kcal/mol
Surface area19600 Å2
MethodPISA
2
C: cytidine monophospho-N-acetylneuraminic acid synthetase
D: cytidine monophospho-N-acetylneuraminic acid synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4044
Polymers52,1752
Non-polymers1,2292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-14 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.048, 79.941, 170.251
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
cytidine monophospho-N-acetylneuraminic acid synthetase


Mass: 26087.453 Da / Num. of mol.: 4 / Fragment: Residues 40-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cmas / Plasmid: pGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q99KK2, N-acylneuraminate cytidylyltransferase
#2: Chemical ChemComp-NCC / CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID


Mass: 614.451 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H31N4O16P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: Tris-HCl, sodium citrate, PEG 400, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoirpH8.9
2200 mMsodium cirtate1reservoir
320 %(v/v)PEG4001reservoir
42 mMTris-HCl1droppH8.0
5150 mM1dropNaCl
60.1 mM1dropNaN3
710 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW611.00590, 1.00850, 0.95000
ROTATING ANODERIGAKU RU20021.5418
Detector
IDDetectorDateDetails
1CCDDec 10, 2001mirrors
2IMAGE PLATEFeb 13, 2002mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1GRAPHITE
Radiation wavelength
IDWavelength (Å)Relative weight
11.00591
21.00851
30.951
41.54181
ReflectionResolution: 2.8→50 Å / Num. all: 28530 / Num. obs: 25492 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.089 / Rsym value: 0.098 / Net I/σ(I): 4
Reflection shellHighest resolution: 2.8 Å / Rsym value: 0.321
Reflection shell
*PLUS
Rmerge(I) obs: 0.321

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: HG-MIR structure

Resolution: 2.8→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.304 1364 random
Rwork0.24 --
all-28530 -
obs-25492 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 123 155 7611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0078
X-RAY DIFFRACTIONc_angle_deg1.274
Refinement
*PLUS
Num. reflection Rfree: 1267 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.27

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