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- PDB-4v3c: The structure of alpha2,3-sialyltransferase variant 2 from Pasteu... -

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Basic information

Entry
Database: PDB / ID: 4v3c
TitleThe structure of alpha2,3-sialyltransferase variant 2 from Pasteurella dagmatis in complex with the donor product CMP
ComponentsSIALYLTRANSFERASE
KeywordsTRANSFERASE
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 / Sialyltransferase
Similarity search - Component
Biological speciesPASTEURELLA DAGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPavkov-Keller, T. / Schmoelzer, K. / Czabany, T. / Luley-Goedl, C. / Ribitsch, D. / Schwab, H. / Nidetzky, B. / Gruber, K.
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: Complete Switch from Alpha2,3- to Alpha2,6-Regioselectivity in Pasteurella Dagmatis Beta-D-Galactoside Sialyltransferase by Active-Site Redesign
Authors: Schmoelzer, K. / Czabany, T. / Pavkov-Keller, T. / Luley-Goedl, C. / Ribitsch, D. / Schwab, H. / Gruber, K. / Nidetzky, B.
History
DepositionOct 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9662
Polymers45,6431
Non-polymers3231
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.750, 111.750, 65.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein SIALYLTRANSFERASE


Mass: 45642.938 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PASTEURELLA DAGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: K9UUI6
#2: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / 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.: 297 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 6.7 MG/ML PROTEIN CONCENTRATION 0.1M SODIUM CITRATE, 20% W/V PEG 3000, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.84→96 Å / Num. obs: 44015 / % possible obs: 99.5 % / Observed criterion σ(I): 1.8 / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4V2U

4v2u


Resolution: 1.84→96 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.749 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21796 2006 5 %RANDOM
Rwork0.17277 ---
obs0.17503 38225 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.84→96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 21 297 3545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193355
X-RAY DIFFRACTIONr_bond_other_d0.0010.023185
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9654539
X-RAY DIFFRACTIONr_angle_other_deg0.82937369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7625393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13224.847163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00615619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5981510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1313.7591566
X-RAY DIFFRACTIONr_mcbond_other3.1243.7571565
X-RAY DIFFRACTIONr_mcangle_it4.2845.6211961
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1464.2221789
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 158 -
Rwork0.304 2796 -
obs--99.49 %

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