[English] 日本語
Yorodumi
- PDB-2x61: Crystal structure of the sialyltransferase CST-II in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x61
TitleCrystal structure of the sialyltransferase CST-II in complex with trisaccharide acceptor and CMP
ComponentsALPHA-2,3-/2,8-SIALYLTRANSFERASE
KeywordsTRANSFERASE / GTA / GLYCOSYLTRANSFERASE
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
ACETATE ION / N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE / Alpha-2,3-/2,8-sialyltransferase
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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.
History
DepositionFeb 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Oct 19, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,22412
Polymers60,8072
Non-polymers2,41710
Water4,738263
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)126,80328
Polymers121,6144
Non-polymers5,18924
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 area16150 Å2
ΔGint-59.7 kcal/mol
Surface area42440 Å2
MethodPISA
2
B: ALPHA-2,3-/2,8-SIALYLTRANSFERASE
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)126,09420
Polymers121,6144
Non-polymers4,48016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation3_565-y,x+1,z1
Buried area14240 Å2
ΔGint-22.7 kcal/mol
Surface area42460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.665, 117.665, 46.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 30403.531 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-258 / 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, Transferases; Glycosyltransferases; Transferring other glycosyl groups
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 271 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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
#5: Chemical ChemComp-CH / N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O8P
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLY ENGINEERED RESIDUE IN CHAIN B, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN B, GLU 222 TO GLY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM HEPES5, PH 7.5, 8% (W/V) POLYETHYLENE GLYCOL 6000, AND 5% (V/V) 2-METHYL-2, 4-PENTANEDIOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2008 / Details: VERTICALLY FOCUSSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 46782 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 38.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RO8

1ro8


Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.39 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19752 2368 5.1 %RANDOM
Rwork0.16389 ---
obs0.16553 44408 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.496 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2---1.94 Å20 Å2
3---3.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 162 263 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224361
X-RAY DIFFRACTIONr_bond_other_d00.023707
X-RAY DIFFRACTIONr_angle_refined_deg1.0682.0025894
X-RAY DIFFRACTIONr_angle_other_deg0.6123.0038595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4195486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59824.955222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84815730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.218156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024693
X-RAY DIFFRACTIONr_gen_planes_other00.02925
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_it0.5041.52447
X-RAY DIFFRACTIONr_mcbond_other0.111.5984
X-RAY DIFFRACTIONr_mcangle_it0.99823934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.55431914
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5384.51958
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 161 -
Rwork0.239 3124 -
obs--96.87 %
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)
11.3057-0.29350.13661.6129-0.64940.7631-0.01290.11260.0252-0.12680.03730.17550.0472-0.0544-0.02430.1022-0.0075-0.01030.1135-0.01180.1339-32.479610.96742.2903
20.69040.9293-0.08982.1569-0.11670.2639-0.0115-0.0331-0.0360.0107-0.0047-0.13090.02430.07910.01620.1050.00920.00150.126-0.00320.1388-13.35857.32326.9471
31.46040.34680.12330.7567-0.03070.08010.0273-0.0150.2104-0.01740.0030.0979-0.0632-0.0094-0.03030.1260.00670.00070.10480.00210.1526-20.835922.07514.8008
49.0994-0.89283.56097.17850.756.5101-0.3838-0.60230.22590.74830.25960.1777-0.33430.05860.12420.15330.04960.03820.1752-0.03990.1059-32.784111.675521.7297
53.9661-0.89180.40182.20680.75892.87850.03490.09820.455-0.06060.015-0.003-0.2060.0136-0.04990.11470.0014-0.00090.08130.0450.1957-19.5628.3557-1.3167
60.8582-0.38040.09530.6193-0.30671.02190.08010.14840.2646-0.08690.03150.2086-0.0043-0.1761-0.11160.11020.0413-0.060.15210.08230.3419-36.589826.5615-4.9866
73.496-1.97661.68272.8113-1.68763.3559-0.2302-0.3674-0.00740.29680.20160.1407-0.0959-0.13180.02850.1312-0.0170.0460.0806-0.02020.1276-30.31291.832915.9238
81.56710.54550.53751.58520.35640.70520.02770.0896-0.3189-0.03110.0299-0.04430.02470.0389-0.05760.09230.0208-0.00310.08820.01970.2154-56.894524.222215.1222
92.8458-0.03150.24760.5322-0.13620.1025-0.0094-0.09920.06940.10010.0080.0483-0.0552-0.00180.00140.12150.00310.00080.10330.0160.1469-60.603643.415219.791
101.0009-0.4611-0.16381.55920.41370.15530.0055-0.0533-0.24370.08650.0070.19280.0392-0.0282-0.01250.0952-0.01390.00160.11120.03220.2012-72.262532.313216.9731
113.25483.21380.86887.24875.07647.1180.2352-0.6-0.11910.7188-0.39120.27710.111-0.41030.1560.23590.0196-0.00150.2320.10770.2441-57.531622.735933.3844
123.52020.4206-0.75445.3602-2.77127.4091-0.02170.0041-0.4483-0.02460.01340.50910.2955-0.39510.00830.0657-0.02460.00520.0567-0.00780.2819-78.907631.516112.716
131.81030.62520.89411.35510.31161.00880.09930.0422-0.46440.03010.0138-0.03280.23770.0749-0.11310.09670.0185-0.00560.03530.03760.2286-61.368420.229915.6272
1415.2684-1.0635-2.10610.9809-1.45713.1395-0.3971-0.7938-0.05540.24980.37020.0217-0.2694-0.49120.02690.502-0.04350.25040.4778-0.10570.4475-53.355743.562532.1831
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 79
2X-RAY DIFFRACTION2A80 - 113
3X-RAY DIFFRACTION3A114 - 166
4X-RAY DIFFRACTION4A167 - 178
5X-RAY DIFFRACTION5A189 - 210
6X-RAY DIFFRACTION6A211 - 234
7X-RAY DIFFRACTION7A235 - 258
8X-RAY DIFFRACTION8B2 - 77
9X-RAY DIFFRACTION9B78 - 113
10X-RAY DIFFRACTION10B114 - 163
11X-RAY DIFFRACTION11B164 - 177
12X-RAY DIFFRACTION12B189 - 205
13X-RAY DIFFRACTION13B206 - 253
14X-RAY DIFFRACTION14B254 - 258

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more