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- PDB-4v2u: Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis -

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Basic information

Entry
Database: PDB / ID: 4v2u
TitleApo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis
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
Biological speciesPASTEURELLA DAGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Data collection
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIALYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)45,6621
Polymers45,6621
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.724, 56.590, 79.542
Angle α, β, γ (deg.)90.00, 111.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SIALYLTRANSFERASE


Mass: 45662.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PASTEURELLA DAGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: K9UUI6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 3.3 MG/ML OF PROTEIN INDEX SCREEN CONDITION D9 (0.1M TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332
DetectorType: PILATUS / Detector: PIXEL / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.71→45.1 Å / Num. obs: 12618 / % possible obs: 98.8 % / Observed criterion σ(I): 1.9 / Redundancy: 3.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 2.71→2.87 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3

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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 2ILV

2ilv


Resolution: 2.71→45.11 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / SU B: 16.81 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY RESIDUES 36-39 ARE DISORDERED OR SHOW MULTIPLE CONFORMATIONS AND COULD NOT BE BUILD WITH CERTAINTY
RfactorNum. reflection% reflectionSelection details
Rfree0.26099 631 5 %RANDOM
Rwork0.1863 ---
obs0.19018 11987 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20.64 Å2
2---1.78 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.71→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3207 0 0 11 3218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193287
X-RAY DIFFRACTIONr_bond_other_d0.0010.023135
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9614438
X-RAY DIFFRACTIONr_angle_other_deg0.81837251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4724.907161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99315612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9761510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
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_it3.2474.4131542
X-RAY DIFFRACTIONr_mcbond_other3.2484.4131541
X-RAY DIFFRACTIONr_mcangle_it5.0046.6161924
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5984.7571745
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: 2.708→2.778 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 45 -
Rwork0.37 855 -
obs--96.46 %

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