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- PDB-2ex1: Crystal structure of mutifunctional sialyltransferase from Pasteu... -

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Basic information

Entry
Database: PDB / ID: 2ex1
TitleCrystal structure of mutifunctional sialyltransferase from Pasteurella multocida with CMP bound
Componentsa2,3-sialyltransferase, a2,a6-sialyltransferase
KeywordsTRANSFERASE / two Rossman fold sialyltransferase-CMP complex
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
CYTIDINE-5'-MONOPHOSPHATE / Alpha-2,3/2,6-sialyltransferase/sialidase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 999SEQUENCE Currently there is no sequence database available for the protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: a2,3-sialyltransferase, a2,a6-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5592
Polymers46,2361
Non-polymers3231
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.255, 64.571, 64.840
Angle α, β, γ (deg.)90.00, 98.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein a2,3-sialyltransferase, a2,a6-sialyltransferase


Mass: 46236.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein has four enzymatic activites / 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: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
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, 2 mM CMP-sialic acid, 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: 0.97931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 22, 2005 / Details: Mar325
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2→64.15 Å / Num. all: 33988 / Num. obs: 33403 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.059 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2457 / Rsym value: 0.24 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EX0

1ex0


Resolution: 2→38.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1277163.39 / 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
Rfree0.222 1731 5.2 %RANDOM
Rwork0.192 ---
all0.195 33988 --
obs0.192 33403 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.2631 Å2 / ksol: 0.3773 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.51 Å20 Å28.07 Å2
2---1.51 Å20 Å2
3----5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 21 398 3528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 309 5.6 %
Rwork0.232 5226 -
obs-5535 97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3c5p_xplor_pac5p_xplor.top

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