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- PDB-3s44: Crystal Structure of Pasteurella multocida sialyltransferase M144... -

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Basic information

Entry
Database: PDB / ID: 3s44
TitleCrystal Structure of Pasteurella multocida sialyltransferase M144D mutant with CMP bound
ComponentsAlpha-2,3/2,6-sialyltransferase/sialidase
KeywordsTRANSFERASE / GT-B fold / Sialyltransferase
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
CMP-3F(a)-Neu5Ac / Alpha-2,3/2,6-sialyltransferase/sialidase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSugiarto, G. / Lau, K. / Li, Y. / Lim, S. / Ames, J.B. / Le, D.-T. / Fisher, A.J. / Chen, X.
CitationJournal: Acs Chem.Biol. / Year: 2012
Title: A Sialyltransferase Mutant with Decreased Donor Hydrolysis and Reduced Sialidase Activities for Directly Sialylating Lewis(x).
Authors: Sugiarto, G. / Lau, K. / Qu, J. / Li, Y. / Lim, S. / Mu, S. / Ames, J.B. / Fisher, A.J. / Chen, X.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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

Downloads & links

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Assembly

Deposited unit
A: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0402
Polymers46,4511
Non-polymers5881
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.440, 61.570, 62.580
Angle α, β, γ (deg.)90.00, 114.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-2,3/2,6-sialyltransferase/sialidase


Mass: 46451.355 Da / Num. of mol.: 1 / Fragment: UNP residues 26-412 / Mutation: M144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: P-1059 / Gene: homologue of Pm0188 / Plasmid: pET23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15KI8, EC: 2.4.99.-
#2: Chemical ChemComp-FN5 / CMP-3F(a)-Neu5Ac


Mass: 588.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30FN4O14P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 38.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG3350, 50 mM sodium chloride, 0.4% Triton X-100, 100 mM HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 24, 2010
RadiationMonochromator: Si 111 Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. all: 64577 / Num. obs: 63327 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 19.06
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.58 / Num. unique all: 5052 / % possible all: 98.2

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IHJ

2ihj


Resolution: 1.45→23.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.995 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21482 3230 5.1 %RANDOM
Rwork0.18701 ---
obs0.18842 63327 98.25 %-
all-64577 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20.06 Å2
2--0.81 Å20 Å2
3----0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.079 Å-
Luzzati sigma a-0.053 Å
Refinement stepCycle: LAST / Resolution: 1.45→23.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 21 431 3637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9584483
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.96725.294170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57615575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9811511
X-RAY DIFFRACTIONr_chiral_restr0.1020.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212520
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8321.51948
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45723168
X-RAY DIFFRACTIONr_scbond_it2.46331351
X-RAY DIFFRACTIONr_scangle_it3.864.51312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 239 -
Rwork0.281 4436 -
obs--98.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7965-0.19490.70960.5651-0.18270.9310.0449-0.1183-0.18660.03260.00920.08030.1064-0.0277-0.0540.02830.00510.01380.01870.02470.042814.26678.192218.2893
21.57390.4879-0.12760.5937-0.09970.9324-0.0518-0.00170.0208-0.03550.04060.11020.0078-0.07720.01130.01810.00480.00260.01620.02320.0683.515216.724712.2366
31.10640.4756-0.37671.58410.1950.3176-0.16350.2263-0.0698-0.19640.1209-0.1042-0.01530.03650.04260.1488-0.07050.00720.16530.02670.053721.268114.5918-16.5468
41.90220.7632-0.35271.15550.42461.6493-0.16870.1360.1289-0.17750.04620.193-0.1303-0.07530.12250.0965-0.0238-0.04960.02530.01990.04868.114117.4342-11.1645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 152
2X-RAY DIFFRACTION2A153 - 250
3X-RAY DIFFRACTION3A251 - 333
4X-RAY DIFFRACTION4A334 - 412

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