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- PDB-2z4t: Crystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2... -

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Basic information

Entry
Database: PDB / ID: 2z4t
TitleCrystal Structure of Vibrionaceae Photobacterium sp. JT-ISH-224 2,6-sialyltransferase in a Ternary Complex with Donor Product CMP and Accepter Substrate Lactose
ComponentsBeta-galactoside alpha-2,6-sialyltransferase
KeywordsTRANSFERASE / GT-B fold / immunoglobulin-like beta-sandwich fold / Glycosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
Immunoglobulin-like - #3010 / 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 / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich ...Immunoglobulin-like - #3010 / 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 / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-lactose / CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / Beta-galactoside alpha-2,6-sialyltransferase
Similarity search - Component
Biological speciesPhotobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKakuta, Y. / Okino, N. / Kajiwara, H. / Ichikawa, M. / Takakura, Y. / Ito, M. / Yamamoto, T.
CitationJournal: Glycobiology / Year: 2008
Title: Crystal structure of Vibrionaceae Photobacterium sp. JT-ISH-224 alpha2,6-sialyltransferase in a ternary complex with donor product CMP and acceptor substrate lactose: catalytic mechanism and substrate recognition
Authors: Kakuta, Y. / Okino, N. / Kajiwara, H. / Ichikawa, M. / Takakura, Y. / Ito, M. / Yamamoto, T.
History
DepositionJun 25, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactoside alpha-2,6-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,96113
Polymers58,5721
Non-polymers1,38912
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.292, 90.292, 204.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-galactoside alpha-2,6-sialyltransferase /


Mass: 58571.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium sp. (bacteria) / Strain: JT-ISH-224 / Gene: pst6-224 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: A8QYL1
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 292 molecules

#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 4.11 Å3/Da / Density % sol: 70.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M lithium sulfate, 30% PEG4000, 0.1M Tris-HCl (pH8.5), VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 34277 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.432 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EX1

2ex1


Resolution: 2.5→41.31 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.178 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.266 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24297 1727 5.1 %RANDOM
Rwork0.19217 ---
obs0.19467 32443 99.84 %-
all-32443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 87 281 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224198
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9645717
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.2885510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.91226205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1215725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.2861511
X-RAY DIFFRACTIONr_chiral_restr0.180.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023142
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.22178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22836
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2326
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.52554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19624088
X-RAY DIFFRACTIONr_scbond_it1.62631848
X-RAY DIFFRACTIONr_scangle_it2.6484.51621
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 132 -
Rwork0.262 2349 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 22.801 Å / Origin y: -36.102 Å / Origin z: -20.571 Å
111213212223313233
T-0.0385 Å2-0.0063 Å2-0.0007 Å2--0.2049 Å20.0051 Å2---0.281 Å2
L1.1437 °20.8178 °20.3862 °2-0.9091 °20.3454 °2--0.4668 °2
S0.1307 Å °0.038 Å °-0.0551 Å °0.0919 Å °-0.0036 Å °-0.0341 Å °0.0447 Å °0.0004 Å °-0.1271 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 9822 - 98
2X-RAY DIFFRACTION1AA99 - 30299 - 302
3X-RAY DIFFRACTION1AA303 - 498303 - 498

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