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- PDB-2p56: Crystal structure of alpha-2,3-sialyltransferase from Campylobact... -

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Basic information

Entry
Database: PDB / ID: 2p56
TitleCrystal structure of alpha-2,3-sialyltransferase from Campylobacter jejuni in apo form
ComponentsAlpha-2,3-sialyltransferase
KeywordsTRANSFERASE / mixed alpha beta
Function / homology
Function and homology information


glycosyltransferase activity / membrane
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
Alpha-2,3-sialyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChiu, C.P. / Lairson, L.L. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Analysis of the alpha-2,3-Sialyltransferase Cst-I from Campylobacter jejuni in Apo and Substrate-Analogue Bound Forms.
Authors: Chiu, C.P. / Lairson, L.L. / Gilbert, M. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1406
Polymers33,8301
Non-polymers3105
Water1,51384
1
A: Alpha-2,3-sialyltransferase
hetero molecules

A: Alpha-2,3-sialyltransferase
hetero molecules

A: Alpha-2,3-sialyltransferase
hetero molecules

A: Alpha-2,3-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,56124
Polymers135,3194
Non-polymers1,24120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area9680 Å2
ΔGint8 kcal/mol
Surface area45920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.396, 112.396, 58.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: xyz, -x-y-z, -yxz, y-xz

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Components

#1: Protein Alpha-2,3-sialyltransferase


Mass: 33829.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cst-I / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q9RGF1, EC: 2.4.99.-
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growpH: 7.5 / Details: 20mM Tris-HCl pH 7.5, and 200mM NaCl

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.514
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 18129 / % possible obs: 96.5 % / Rmerge(I) obs: 0.057 / Rsym value: 0.043 / Χ2: 0.984 / Net I/σ(I): 18.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.236 / Num. unique all: 1245 / Rsym value: 0.214 / Χ2: 1.029 / % possible all: 66.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1RO7

1ro7


Resolution: 2.2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25 879 4.7 %Random
Rwork0.212 ---
all0.214 18129 --
obs0.214 18129 96.6 %-
Solvent computationBsol: 43.922 Å2
Displacement parametersBiso mean: 40.21 Å2
Baniso -1Baniso -2Baniso -3
1-10.082 Å20 Å20 Å2
2--10.082 Å20 Å2
3----20.164 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 20 84 2232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.191
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4edo.par

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