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- PDB-2x63: Crystal structure of the sialyltransferase CST-II N51A in complex... -

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Basic information

Entry
Database: PDB / ID: 2x63
TitleCrystal structure of the sialyltransferase CST-II N51A in complex with CMP
ComponentsALPHA-2,3-/2,8-SIALYLTRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / GTA
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, H.J. / Lairson, L.L. / Rich, J.R. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Kinetic Analysis of Substrate Binding to the Sialyltransferase Cst-II from Campylobacter Jejuni.
Authors: Lee, H.J. / Lairson, L.L. / Rich, J.R. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.
History
DepositionFeb 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Version format compliance
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7293
Polymers30,3431
Non-polymers3852
Water3,171176
1
A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE
hetero molecules

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE
hetero molecules

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE
hetero molecules

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,91512
Polymers121,3744
Non-polymers1,5418
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9150 Å2
ΔGint-24.5 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.190, 116.190, 46.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein ALPHA-2,3-/2,8-SIALYLTRANSFERASE / ALPHA-2\ / 3/8-SIALYLTRANSFERASE / SIALYLTRANSFERASE CST-II


Mass: 30343.414 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-259 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Strain: OH4384 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LAK3, EC: 2.4.99.-
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 51 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ASN 51 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLY
Sequence details32 RESIDUES DELETED AT THE C-TERMINUS

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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: 2.48 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM HEPES5, PH 7.5, 8% (W/V) POLYETHYLENE GLYCOL 6000, 5% (V/V) 2-METHYL-2,4-PENTANEDIOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 2008 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 21401 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RO8

1ro8


Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.351 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23005 1098 5.1 %RANDOM
Rwork0.18565 ---
obs0.18788 20305 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 24.557 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2---1.42 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2147 0 25 176 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222244
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9593034
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2665263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0725118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10115382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.821153
X-RAY DIFFRACTIONr_chiral_restr0.0730.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211733
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3931.51295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7522088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2993949
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0394.5943
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 87 -
Rwork0.256 1468 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9085-0.63290.8693.35531.14244.7092-0.1265-0.1479-0.280.14530.045-0.37840.0969-0.15740.08150.0440.0033-0.01960.06480.04350.133135.6467-12.9207-9.3698
29.8172-1.3137.32731.6771-0.71395.529-0.0015-1.0483-0.3470.44070.3044-0.42090.0623-0.7097-0.30280.12920.0323-0.1430.29050.07820.204939.8143-15.6491-2.3027
32.2858-0.56870.51221.09040.13520.30970.019-0.0361-0.3270.06490.0073-0.07390.03950.036-0.02620.07070.00490.01040.0520.04060.132824.6278-17.6156-15.5856
41.42330.9340.0852.54140.54650.18240.0101-0.01880.04450.0715-0.03-0.0166-0.0304-0.0270.020.09750.0125-0.00370.09810.01530.039114.9457-4.9116-14.6738
51.4663-0.4898-0.09981.9257-0.63340.8529-0.0082-0.08430.03890.025-0.0498-0.34440.02610.09550.0580.0558-0.0128-0.02360.08130.01330.07930.1562-1.315-13.8701
63.4027-0.10461.44034.30060.37814.4309-0.23560.832-0.1304-0.34620.1754-0.6059-0.36450.49950.06020.0696-0.07520.05450.2215-0.05050.103232.6385-14.9866-29.5167
71.349-0.85140.56811.8987-0.68491.2298-0.0598-0.15610.1560.06790.0101-0.51240.02320.12140.04960.022-0.0069-0.04180.08520.01440.18138.4039-3.5873-8.114
86-1.15861.95372.0828-0.22443.19860.11440.4629-0.1203-0.0515-0.1359-0.12440.07080.21280.02150.0904-0.01640.05210.06830.00290.069320.8581-22.3805-24.968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION2A15 - 26
3X-RAY DIFFRACTION3A27 - 85
4X-RAY DIFFRACTION4A86 - 118
5X-RAY DIFFRACTION5A119 - 159
6X-RAY DIFFRACTION6A160 - 184
7X-RAY DIFFRACTION7A185 - 233
8X-RAY DIFFRACTION8A234 - 259

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