[English] 日本語
Yorodumi
- PDB-5t5d: Crystal Structure of the PTS IIB protein associated with the fuco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5t5d
TitleCrystal Structure of the PTS IIB protein associated with the fucose utilization operon from Streptococcus pneumoniae
ComponentsPTS system, IIB component
KeywordsTRANSPORT PROTEIN / transport
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / : / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system, IIB component
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHiggins, M.A. / Boraston, A.B.
CitationJournal: Proteins / Year: 2017
Title: Structural characterization of the PTS IIA and IIB proteins associated with pneumococcal fucose utilization.
Authors: Higgins, M.A. / Hamilton, A.M. / Boraston, A.B.
History
DepositionAug 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS system, IIB component


Theoretical massNumber of molelcules
Total (without water)18,5141
Polymers18,5141
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.503, 42.503, 292.922
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21A-256-

HOH

-
Components

#1: Protein PTS system, IIB component


Mass: 18513.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_2163 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2USH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 30% PEG400, 0.2 M Magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9761 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9761 Å / Relative weight: 1
ReflectionResolution: 2.5→37 Å / Num. obs: 67795 / % possible obs: 99.2 % / Redundancy: 10.94 % / Net I/σ(I): 14.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.809 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.98
RfactorNum. reflection% reflection
Rfree0.2971 283 4.61 %
Rwork0.2236 --
obs0.2277 6143 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 0 57 1192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091152
X-RAY DIFFRACTIONf_angle_d0.9581564
X-RAY DIFFRACTIONf_dihedral_angle_d15.877692
X-RAY DIFFRACTIONf_chiral_restr0.056190
X-RAY DIFFRACTIONf_plane_restr0.007197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-3.14960.34371380.20652794X-RAY DIFFRACTION100
3.1496-36.81270.28461450.22833066X-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)
10.6261-0.0295-0.61460.42330.4961.02420.36580.13311.1074-0.0127-0.1907-0.5282-0.4632-0.40920.00040.6376-0.0431-0.00490.4523-0.00630.56296.052416.664513.3653
21.2844-0.2716-0.61971.1441-0.98061.35550.1990.05720.0681-0.1328-0.4467-0.3013-0.4508-0.1240.00060.6553-0.0093-0.00080.45860.03440.504311.41817.81923.5068
32.1399-0.8411-0.54192.14730.47321.79430.1343-0.3331-0.0673-0.0593-0.1806-0.27120.23220.2311-00.5842-0.01310.00430.32730.05680.466215.81617.077411.0054
41.2299-2.1371-0.25543.73570.1872.93510.63590.1075-1.73640.07140.27420.6989-1.0769-1.2820.14220.7288-0.1526-0.05210.57110.20760.7921-4.4534.01359.8407
50.64730.7811-0.05051.1853-0.48741.2904-0.01990.02620.1814-0.2956-0.26260.6130.3401-0.3543-0.00120.606-0.0385-0.01680.37340.0390.50882.24851.842216.8608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 156 )

+
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