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- PDB-2ex0: Crystal structure of multifunctional sialyltransferase from Paste... -

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Basic information

Entry
Database: PDB / ID: 2ex0
TitleCrystal structure of multifunctional sialyltransferase from Pasteurella Multocida
Componentsa2,3-sialyltransferase, a2,6-sialyltransferase
KeywordsTRANSFERASE / two Rossman fold
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Sialyltransferase, C-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Sialyltransferase, N-terminal GT-B Rossman nucleotide-binding domain / Sialyltransferase PMO188 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-2,3/2,6-sialyltransferase/sialidase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNi, L. / Sun, M. / Chen, X. / Fisher, A.J.
CitationJournal: Biochemistry / Year: 2006
Title: Cytidine 5'-Monophosphate (CMP)-Induced Structural Changes in a Multifunctional Sialyltransferase from Pasteurella multocida
Authors: Ni, L. / Sun, M. / Yu, H. / Chokhawala, H. / Chen, X. / Fisher, A.J.
History
DepositionNov 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Currently there is no aminoacid sequence database reference available for this protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: a2,3-sialyltransferase, a2,6-sialyltransferase
B: a2,3-sialyltransferase, a2,6-sialyltransferase


Theoretical massNumber of molelcules
Total (without water)92,9352
Polymers92,9352
Non-polymers00
Water15,151841
1
A: a2,3-sialyltransferase, a2,6-sialyltransferase


Theoretical massNumber of molelcules
Total (without water)46,4671
Polymers46,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: a2,3-sialyltransferase, a2,6-sialyltransferase


Theoretical massNumber of molelcules
Total (without water)46,4671
Polymers46,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.718, 61.281, 96.649
Angle α, β, γ (deg.)90.00, 101.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein a2,3-sialyltransferase, a2,6-sialyltransferase


Mass: 46467.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein has four enzymatic activities / Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: Pm70 / Gene: Pm0188 / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q15KI8, EC: 2.4.99.4, EC: 2.4.99.6, EC: 2.4.99.9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.216 mM protein, 26% PEG3350, 0.1M NaCl, 0.4% Triton-X-100, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 2005 / Details: Mar325
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→62.38 Å / Num. all: 87948 / Num. obs: 86251 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.069 / Net I/σ(I): 15.1
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5305 / Rsym value: 0.308 / % possible all: 82.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→43.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1183839.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 4349 5 %RANDOM
Rwork0.193 ---
all0.196 87948 --
obs0.193 86251 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8488 Å2 / ksol: 0.350294 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.5 Å2
2--2.87 Å20 Å2
3----2.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.65→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6371 0 0 841 7212
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 646 5 %
Rwork0.275 12404 -
obs-13050 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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