[English] 日本語
Yorodumi
- PDB-2wqq: Crystallographic analysis of monomeric CstII -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wqq
TitleCrystallographic analysis of monomeric CstII
ComponentsALPHA-2,3-/2,8-SIALYLTRANSFERASE
KeywordsTRANSFERASE / GTA / CSTII / SIALYLTRANSFERASE / 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
Chem-CSF / DI(HYDROXYETHYL)ETHER / Alpha-2,3-/2,8-sialyltransferase
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChan, P.H.W. / Lairson, L.L. / Lee, H.J. / Wakarchuk, W.W. / Strynadka, N.C.J. / Withers, S.G. / McIntosh, L.P.
CitationJournal: Biochemistry / Year: 2009
Title: NMR Spectroscopic Characterization of the Sialyltransferase Cstii from Camplyobacter Jejuni: Histidine 188 is the General Base.
Authors: Chan, P.H.W. / Lairson, L.L. / Lee, H.J. / Wakarchuk, W.W. / Strynadka, N.C.J. / Withers, S.G. / Mcintosh, L.P.
History
DepositionAug 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Apr 1, 2015Group: Database references
Revision 1.4Dec 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,1963
Polymers34,4571
Non-polymers7392
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.634, 116.634, 45.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

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


Mass: 34457.457 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Strain: OH4384 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LAK3, EC: 2.4.99.-
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, TYR 125 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, TYR 125 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M AMMONIUM CITRATE TRIBASIC, 10% PEG 3350, PH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 2009 / 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: 2.25→34 Å / Num. obs: 14714 / % possible obs: 100 % / Observed criterion σ(I): 3.5 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RO7

1ro7


Resolution: 2.25→34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 12.898 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21863 743 5 %RANDOM
Rwork0.17659 ---
obs0.17868 13972 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: 19.429 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å20 Å2
2---2.21 Å20 Å2
3---4.42 Å2
Refinement stepCycle: LAST / Resolution: 2.25→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 49 77 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222151
X-RAY DIFFRACTIONr_bond_other_d00.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9772902
X-RAY DIFFRACTIONr_angle_other_deg0.6353.0024278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31924.955111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11515367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.551153
X-RAY DIFFRACTIONr_chiral_restr0.0770.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022334
X-RAY DIFFRACTIONr_gen_planes_other00.02461
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_it0.511.51220
X-RAY DIFFRACTIONr_mcbond_other0.1251.5494
X-RAY DIFFRACTIONr_mcangle_it0.95221963
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5283931
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4074.5939
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: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 74 -
Rwork0.226 988 -
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)
15.0296-0.50392.07085.56392.15177.76470.18230.4888-1.1671-0.1853-0.0241-0.28240.37440.2064-0.15820.08830.0448-0.0320.1288-0.22230.481612.952-39.0543-17.9372
25.0552-1.20941.2285.22041.1941.79740.20260.4517-0.5537-0.222-0.0115-0.36880.09170.1995-0.19110.0790.057-0.00090.0842-0.06910.130819.2454-26.9275-12.2911
35.8081.1064-0.13021.71520.03990.74460.11790.1126-0.1123-0.0397-0.01360.17270.06380.0337-0.10430.08150.0294-0.00440.0322-0.00180.06181.7903-17.8986-8.3229
46.2201-0.2262-1.84523.0379-0.11126.16560.16280.6135-1.0495-0.2098-0.120.40650.0541-0.0417-0.04280.14580.0344-0.06020.1549-0.15320.25173.5809-27.0691-16.759
54.59490.8513.23794.35412.80114.28330.194-0.2719-1.07120.6940.01260.10460.6991-0.0417-0.20660.21610.06920.04430.08320.06560.522611.3925-34.6287-2.505
67.6469-3.6086-1.38414.5548-0.23590.74460.33161.1197-1.4539-0.34-0.3990.84810.1933-0.24660.06740.22560.0171-0.1830.2415-0.26310.4328-2.803-33.7349-18.9944
76.8934-3.94241.36162.5264-0.57692.38070.17650.6879-1.4456-0.2064-0.39270.80780.78030.12720.21620.52990.10670.03120.2004-0.36680.859311.7433-43.5102-20.2425
83.5304-1.8031-0.75659.94054.73146.4077-0.2934-0.2169-0.09010.88330.29-0.46250.2993-0.04760.00340.08760.0418-0.03740.09720.03830.082822.1472-20.12980.4134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 20
2X-RAY DIFFRACTION2A21 - 74
3X-RAY DIFFRACTION3A75 - 128
4X-RAY DIFFRACTION4A129 - 147
5X-RAY DIFFRACTION5A148 - 191
6X-RAY DIFFRACTION6A192 - 211
7X-RAY DIFFRACTION7A212 - 235
8X-RAY DIFFRACTION8A236 - 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://pdbjlc1.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