[English] 日本語
Yorodumi
- PDB-3qkw: Structure of Streptococcus parasangunini Gtf3 glycosyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qkw
TitleStructure of Streptococcus parasangunini Gtf3 glycosyltransferase
ComponentsNucleotide sugar synthetase-like protein
KeywordsTRANSFERASE / GT-B fold / glycosyltransferase / NUCLEOTIDE SUGAR SYNTHETASE-LIKE PROTEIN
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / protein glycosylation / nucleotide binding
Similarity search - Function
Glucosyltransferase 3 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glucosyltransferase 3
Similarity search - Component
Biological speciesStreptococcus parasanguinis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.287 Å
AuthorsZhu, F. / Erlandsen, H. / Huang, Y. / Ding, L. / Zhou, M. / Liang, X. / Ma, J.-B. / Wu, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Analysis of a New Subfamily of Glycosyltransferases Required for Glycosylation of Serine-rich Streptococcal Adhesins.
Authors: Zhu, F. / Erlandsen, H. / Ding, L. / Li, J. / Huang, Y. / Zhou, M. / Liang, X. / Ma, J. / Wu, H.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleotide sugar synthetase-like protein
B: Nucleotide sugar synthetase-like protein
C: Nucleotide sugar synthetase-like protein
D: Nucleotide sugar synthetase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6888
Polymers153,0724
Non-polymers1,6174
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-72 kcal/mol
Surface area47860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.217, 99.244, 188.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Nucleotide sugar synthetase-like protein


Mass: 38267.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus parasanguinis (bacteria) / Gene: nss / Plasmid: pET-SUMO-Gtf3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold (DE3) / References: UniProt: B5A7L9
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 ul of protein solution (15 mg/ml protein and 10mM UDP-Glucose) was mixed with 1 ul of reservoir (0.1M Succinic Acid, 11% Polyethylene glycol 3,350, 10% glycerol), pH 7.0, VAPOR DIFFUSION, ...Details: 1 ul of protein solution (15 mg/ml protein and 10mM UDP-Glucose) was mixed with 1 ul of reservoir (0.1M Succinic Acid, 11% Polyethylene glycol 3,350, 10% glycerol), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2010
RadiationMonochromator: Double crystal - liquid nitrogen cooled / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→42.512 Å / Num. obs: 63229 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 10.8 / % possible all: 96

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_351)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A SAD dataset was collected using Se-Met crystal. Initial structure determined in spacegroup C2221 with Gtf3 dimer.

Resolution: 2.287→42.512 Å / SU ML: 0.37 / Isotropic thermal model: Anisotropic / σ(F): 1.34 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 3217 5.09 %
Rwork0.187 --
obs0.1901 63229 95.69 %
all-63229 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.737 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.6213 Å2-0 Å2-0 Å2
2---5.2667 Å20 Å2
3----7.3547 Å2
Refinement stepCycle: LAST / Resolution: 2.287→42.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10583 0 100 188 10871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810987
X-RAY DIFFRACTIONf_angle_d1.14514894
X-RAY DIFFRACTIONf_dihedral_angle_d17.214090
X-RAY DIFFRACTIONf_chiral_restr0.0771637
X-RAY DIFFRACTIONf_plane_restr0.0051888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.287-2.36920.3472720.25945227X-RAY DIFFRACTION85
2.3692-2.46410.33493020.23855590X-RAY DIFFRACTION90
2.4641-2.57620.33243260.23455850X-RAY DIFFRACTION94
2.5762-2.7120.30973290.2275922X-RAY DIFFRACTION96
2.712-2.88190.29423140.22025981X-RAY DIFFRACTION96
2.8819-3.10440.30643070.22276127X-RAY DIFFRACTION97
3.1044-3.41660.2723170.20286184X-RAY DIFFRACTION99
3.4166-3.91070.22733540.16626253X-RAY DIFFRACTION99
3.9107-4.9260.19913290.14176321X-RAY DIFFRACTION100
4.926-42.51880.19463670.15846557X-RAY DIFFRACTION100
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)
10.3872-0.1982-0.12840.6585-0.04110.4673-0.00720.0158-0.02480.00210.09870.16650.0122-0.05710.25560.1849-0.00580.00990.25440.03190.2555-20.197811.8655-35.7629
20.6955-0.32210.39910.4889-0.1320.37390.01780.075-0.02360.05440.0426-0.0429-0.01270.09240.14860.18370.0078-0.03060.192-0.01780.178118.1814-10.7748-32.9353
30.4396-0.23620.18530.5331-0.10790.2641-0.0982-0.16520.14350.4330.0529-0.1419-0.18780.00910.00010.44250.0058-0.09670.2146-0.06680.22729.744719.1676-10.6127
40.4544-0.40270.06450.6507-0.17320.3218-0.089-0.1686-0.19880.29910.1460.24680.0671-0.1099-00.3524-0.02390.10180.28590.07720.3139-14.9586-18.1143-12.3641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:329)
2X-RAY DIFFRACTION2(CHAIN B AND RESID -1:329)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 0:330)
4X-RAY DIFFRACTION4(CHAIN D AND RESID -1:329)

+
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