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- PDB-2iiq: Crystal structure of Pasteurella multocida sialyltransferase in a... -

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Basic information

Entry
Database: PDB / ID: 2iiq
TitleCrystal structure of Pasteurella multocida sialyltransferase in an open conformation with CMP bound
ComponentsAlpha-2,3/2,6-sialyltransferase/sialidase
KeywordsTRANSFERASE / sialyltransferase / CMP / streak seeding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNi, L. / Fisher, A.J.
CitationJournal: To be Published
Title: Structural analysis of multifunctional sialyltransferase from Pasteurella multocida.
Authors: Ni, L. / Huang, S. / Yu, H. / Cao, H. / Sun, M. / Chen, X. / Fisher, A.J.
History
DepositionSep 28, 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 1.2Aug 30, 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_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

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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
B: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5814
Polymers92,9352
Non-polymers6462
Water10,251569
1
A: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7912
Polymers46,4671
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-2,3/2,6-sialyltransferase/sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7912
Polymers46,4671
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.528, 61.572, 119.547
Angle α, β, γ (deg.)90.00, 94.77, 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: 46467.465 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25%, PEG 3350, 0.1 M NaCl, 0.1 M HEPES, 0.4% Triton X-100 streak seeded by apo crystals, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Jun 29, 2006
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→59.55 Å / Num. all: 39043 / Num. obs: 38951 / % possible obs: 99.76 % / Redundancy: 6.16 % / Biso Wilson estimate: 20.54 Å2 / Rsym value: 0.1001 / Net I/σ(I): 5.35
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 1.78 / Num. unique all: 4884 / Rsym value: 0.2421 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EX0

2ex0


Resolution: 2.3→59.55 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.054 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.6 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25554 1705 5 %RANDOM
Rwork0.20766 ---
obs0.21006 32366 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.23 Å2
2--0.39 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6331 0 42 569 6942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226536
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9588877
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6125776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3725.285333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.779151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0271522
X-RAY DIFFRACTIONr_chiral_restr0.0940.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025002
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.23291
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24463
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5061.53978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81426298
X-RAY DIFFRACTIONr_scbond_it1.2432889
X-RAY DIFFRACTIONr_scangle_it1.9824.52578
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 137 -
Rwork0.217 2359 -
obs-2496 100 %
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)
12.5785-0.11440.84560.35990.0321.18320.0344-0.1929-0.06940.0365-0.02770.09160.1031-0.1572-0.0067-0.1047-0.01140.0232-0.1197-0.0097-0.10578.0856-2.070916.2842
22.42210.87520.74681.86260.43972.0318-0.02970.0264-0.0518-0.13550.0318-0.05190.02880.0283-0.0021-0.0676-0.0064-0.0056-0.11730.0137-0.109115.3322.7126-14.0334
32.9734-0.20630.67710.55370.18231.18050.0015-0.2155-0.09510.0951-0.04040.14290.1073-0.17250.0389-0.081-0.01550.0357-0.1027-0.0184-0.0936-12.9485-5.8707-43.1225
42.6480.46240.61311.70070.33432.2070.0035-0.0058-0.1515-0.0976-0.0011-0.04660.05080.041-0.0024-0.0528-0.0108-0.0132-0.11750.0211-0.1051-6.2024-1.0968-73.5633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 2351 - 211
2X-RAY DIFFRACTION2AA250 - 412226 - 388
3X-RAY DIFFRACTION3BB25 - 2351 - 211
4X-RAY DIFFRACTION4BB250 - 412226 - 388

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