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- PDB-1ro7: Structural analysis of the sialyltransferase CstII from Campyloba... -

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Basic information

Entry
Database: PDB / ID: 1ro7
TitleStructural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analogue, CMP-3FNeuAc.
Componentsalpha-2,3/8-sialyltransferase
KeywordsTRANSFERASE / mixed alpha/beta / Rossmann fold
Function / homology
Function and homology information


glycosyltransferase activity
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
Chem-CSF / Alpha-2,3-/2,8-sialyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
Authors: Chiu, C.P. / Watts, A.G. / Lairson, L.L. / Gilbert, M. / Lim, D. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-2,3/8-sialyltransferase
B: alpha-2,3/8-sialyltransferase
C: alpha-2,3/8-sialyltransferase
D: alpha-2,3/8-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5699
Polymers122,9224
Non-polymers2,6485
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-53 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.660, 66.031, 99.172
Angle α, β, γ (deg.)90.00, 94.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
alpha-2,3/8-sialyltransferase


Mass: 30730.379 Da / Num. of mol.: 4 / Mutation: I53S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cst / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9LAK3, Transferases; Glycosyltransferases; Transferring other glycosyl groups
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CSF / CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID / CMP-3FNEUAC


Type: RNA linking / Mass: 632.442 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H30FN4O16P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG MME 2000, sodium chloride, bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
210 mM1dropMgCl2
310 mMdonor1drop
4100 mMbicine1reservoirpH9.0
510 %(w/v)PEG2000 MME1reservoir
6100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 99748 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.054 / Net I/σ(I): 23.6
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.526 / % possible all: 98.5
Reflection
*PLUS
% possible obs: 99.6 % / Num. measured all: 429958 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.526

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.64 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1876668.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5034 5.1 %RANDOM
Rwork0.217 ---
obs0.217 99667 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0095 Å2 / ksol: 0.338876 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.23 Å20 Å2-3.78 Å2
2--5.33 Å20 Å2
3----0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8162 0 168 338 8668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 855 5.2 %
Rwork0.291 15501 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ION.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4LIGAND.PAR&_1_TOPOLOGY_INFILE_4
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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