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- PDB-2drj: Xray structure of alpha-2,3/8-sialyltransferase CstII F91Y mutant -

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Basic information

Entry
Database: PDB / ID: 2drj
TitleXray structure of alpha-2,3/8-sialyltransferase CstII F91Y mutant
ComponentsAlpha-2,3/8-sialyltransferase
KeywordsTRANSFERASE / mixed alpha/beta
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Alpha-2,3-sialyltransferase / Alpha-2,3-sialyltransferase / Alpha-2,3-sialyltransferase superfamily / Alpha-2,3-sialyltransferase (CST-I) / sialyltransferase cstii, chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-CSF / ISOPROPYL ALCOHOL / Alpha-2,3-/2,8-sialyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChiu, C.P.C. / Strynadka, N.C.J.
CitationJournal: Nat.Methods / Year: 2006
Title: High-throughput screening methodology for the directed evolution of glycosyltransferases
Authors: Aharoni, A. / Thieme, K. / Chiu, C.P.C. / Buchini, S. / Lairson, L.L. / Chen, H. / Strynadka, N.C.J. / Wakarchuk, W.W. / Withers, S.G.
History
DepositionJun 9, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-2,3/8-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5694
Polymers30,8161
Non-polymers7533
Water1,65792
1
A: Alpha-2,3/8-sialyltransferase
hetero molecules

A: Alpha-2,3/8-sialyltransferase
hetero molecules

A: Alpha-2,3/8-sialyltransferase
hetero molecules

A: Alpha-2,3/8-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,27416
Polymers123,2644
Non-polymers3,01112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)116.653, 116.653, 44.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer generated from the molecule in the asymmetric unit by the operations: -x,-y,z; -y,x,z; y,-x,z.

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Components

#1: Protein Alpha-2,3/8-sialyltransferase / Alpha-2 / 3-/2 / 8-sialyltransferase


Mass: 30815.912 Da / Num. of mol.: 1 / Fragment: sialyltransferase residues 1-259 / Mutation: F91Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q9LAK3, EC: 2.4.99.-
#2: Chemical ChemComp-CSF / CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID / CMP-3FNEUAC


Type: RNA linking / Mass: 632.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30FN4O16P
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M TEA pH 7.5, 20% PEG 400, 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.514 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2005 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 13458 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Χ2: 0.986 / Net I/σ(I): 23.1
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.185 / Num. unique all: 926 / Χ2: 0.948 / % possible all: 65.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RO7

1ro7


Resolution: 2.25→23.81 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.545 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.261 685 5.1 %RANDOM
Rwork0.194 ---
all0.197 13478 --
obs0.197 12793 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.254 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2---1.92 Å20 Å2
3---3.85 Å2
Refinement stepCycle: LAST / Resolution: 2.25→23.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 42 100 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222053
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.9872775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12624.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.41115349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.049153
X-RAY DIFFRACTIONr_chiral_restr0.1250.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021561
X-RAY DIFFRACTIONr_nbd_refined0.2230.2932
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.210
X-RAY DIFFRACTIONr_mcbond_it1.1871.51203
X-RAY DIFFRACTIONr_mcangle_it2.03321878
X-RAY DIFFRACTIONr_scbond_it3.0293991
X-RAY DIFFRACTIONr_scangle_it4.1834.5897
LS refinement shellResolution: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 33 -
Rwork0.173 647 -
obs-680 100 %

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