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- PDB-2p2v: Crystal structure analysis of monofunctional alpha-2,3-sialyltran... -

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Basic information

Entry
Database: PDB / ID: 2p2v
TitleCrystal structure analysis of monofunctional alpha-2,3-sialyltransferase Cst-I from Campylobacter jejuni
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
Chem-CSF / Alpha-2,3-sialyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 7, 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: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
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)35,24315
Polymers33,8301
Non-polymers1,41314
Water3,603200
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)140,97060
Polymers135,3194
Non-polymers5,65156
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
Unit cell
Length a, b, c (Å)112.388, 112.388, 58.757
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CSF / CYTIDINE-5'-MONOPHOSPHATE-3-FLUORO-N-ACETYL-NEURAMINIC ACID / CMP-3FNEUAC


Type: RNA linking / Mass: 632.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30FN4O16P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growpH: 7.5 / Details: 20mM Tris-HCl pH 7.5, and 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2004 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 40593 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.59 % / Rmerge(I) obs: 0.064 / Χ2: 0.991 / Net I/σ(I): 21.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.760.5242.639650.95499
1.76-1.830.3940350.98399.8
1.83-1.910.27140501.001100
1.91-2.020.19940681.025100
2.02-2.140.14340151.04100
2.14-2.310.1140900.98100
2.31-2.540.09640600.984100
2.54-2.910.08440690.913100
2.91-3.660.06340800.994100
3.66-500.0541611.03399.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1RO7

1ro7


Resolution: 1.85→39.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.268 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1565 5 %RANDOM
Rwork0.202 ---
all0.204 40593 --
obs0.204 31362 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 91 200 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222425
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.9793263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15225.246122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.891154
X-RAY DIFFRACTIONr_chiral_restr0.1250.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021820
X-RAY DIFFRACTIONr_nbd_refined0.2120.21147
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.213
X-RAY DIFFRACTIONr_mcbond_it1.1811.51427
X-RAY DIFFRACTIONr_mcangle_it1.92422239
X-RAY DIFFRACTIONr_scbond_it2.66131143
X-RAY DIFFRACTIONr_scangle_it3.8674.51022
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 124 -
Rwork0.298 2149 -
obs-2273 100 %

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