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- PDB-2ii6: Crystal structure of Pasteurella multocida sialyltransferase D141... -

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Basic information

Entry
Database: PDB / ID: 2ii6
TitleCrystal structure of Pasteurella multocida sialyltransferase D141N mutant in open conformation with CMP bound
ComponentsAlpha-2,3/2,6-sialyltransferase/sialidase
KeywordsTRANSFERASE / mutant D141N / sialyltransferase / streak seeding / CMP / two Rossmann domains
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: 1.75 Å
AuthorsFisher, A.J. / Ni, L.
CitationJournal: To be Published
Title: Structural analysis of multifunctional sialyltransferase from Pasteurella multocida.
Authors: Ni, L. / Huang, S. / Yu, H. / Sun, M. / Cao, H. / Chen, X. / Fisher, A.J.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7902
Polymers46,4661
Non-polymers3231
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.625, 62.049, 61.529
Angle α, β, γ (deg.)90.00, 113.70, 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: 46466.480 Da / Num. of mol.: 1 / Fragment: alpha2,3-silayltransferase / Mutation: D141N
Source method: isolated from a genetically manipulated source
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
#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.: 484 / 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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growpH: 7.5
Details: 25% PEG3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100, pH 7.5

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 6, 2006 / Details: DOUBLE CRYSTAL MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→31.02 Å / Num. all: 36710 / Num. obs: 35649 / % possible obs: 97.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.472 Å2 / Rsym value: 0.107 / Net I/σ(I): 9
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2678 / Rsym value: 0.191 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EX0

2ex0


Resolution: 1.75→31.02 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.563 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24669 1781 5 %RANDOM
Rwork0.20046 ---
obs0.20278 33850 97.08 %-
all-34868 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.673 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.7 Å2
2---0.26 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 21 484 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9584469
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69425.241166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01615565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1561511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022518
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21602
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22290
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2401
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.52010
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06123176
X-RAY DIFFRACTIONr_scbond_it1.831447
X-RAY DIFFRACTIONr_scangle_it2.7074.51293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 128 -
Rwork0.245 2446 -
obs-2574 95.97 %
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)
12.1029-0.00680.03320.42020.1140.6512-0.0372-0.0875-0.06760.0578-0.00860.05130.0401-0.03760.0458-0.08640.00050.0191-0.1412-0.0069-0.13468.5184-1.892515.6715
21.45630.07350.10071.1862-0.02410.76240.014-0.0866-0.0443-0.0034-0.00280.00670.02-0.0077-0.0111-0.0906-0.00960.0077-0.1270.0035-0.13515.74322.6404-13.8336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 2401 - 216
2X-RAY DIFFRACTION2AA248 - 412224 - 388

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