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- PDB-1ro8: Structural analysis of the sialyltransferase CstII from Campyloba... -

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Basic information

Entry
Database: PDB / ID: 1ro8
TitleStructural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analogue, cytidine-5'-monophosphate
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
CYTIDINE-5'-MONOPHOSPHATE / Alpha-2,3-/2,8-sialyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 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 1.3Oct 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 1.4Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,5284
Polymers61,8812
Non-polymers6462
Water1,15364
1
A: alpha-2,3/8-sialyltransferase
hetero molecules

A: alpha-2,3/8-sialyltransferase
hetero molecules

A: alpha-2,3/8-sialyltransferase
hetero molecules

A: alpha-2,3/8-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0558
Polymers123,7624
Non-polymers1,2934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
2
B: alpha-2,3/8-sialyltransferase
hetero molecules

B: alpha-2,3/8-sialyltransferase
hetero molecules

B: alpha-2,3/8-sialyltransferase
hetero molecules

B: alpha-2,3/8-sialyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0558
Polymers123,7624
Non-polymers1,2934
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
Unit cell
Length a, b, c (Å)115.434, 115.434, 41.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
DetailsThe biological assembly is a tetramer generated from one molecule in the asymmetric unit by the operations:

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Components

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


Mass: 30940.596 Da / Num. of mol.: 2 / Mutation: I53S, E222G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: cst / Plasmid: pET28a / 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-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.: 64 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 6000, MPD, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
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 mMHEPES1reservoirpH7.5
510 %(w/v)PEG60001reservoir
65 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97912, 0.97961, 0.97900
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2002 / Details: mirrors
RadiationMonochromator: Si(111), (220) and W-B4C multilayer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.979611
30.9791
ReflectionResolution: 2→30 Å / Num. obs: 62730 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.18 Å / Mean I/σ(I) obs: 10.6 / Rsym value: 0.091 / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→28.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2324601.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2941 4.9 %RANDOM
Rwork0.22 ---
all0.258 ---
obs0.258 60525 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5553 Å2 / ksol: 0.356015 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.28 Å20 Å20 Å2
2---14.85 Å20 Å2
3---30.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.05→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 42 64 4050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 347 5 %
Rwork0.247 6635 -
obs--63.2 %
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 DIFFRACTION4C1PMOD.PAR&_1_TOPOLOGY_INFILE_4
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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