[English] 日本語
Yorodumi
- PDB-4jis: Crystal structure of ribitol 5-phosphate cytidylyltransferase (Ta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jis
TitleCrystal structure of ribitol 5-phosphate cytidylyltransferase (TarI) from Bacillus subtilis
Componentsribitol-5-phosphate cytidylyltransferase
KeywordsTRANSFERASE / ribitol 5-phosphate cytidylyltransferase
Function / homology
Function and homology information


D-ribitol-5-phosphate cytidylyltransferase / D-ribitol-5-phosphate cytidylyltransferase activity / poly(ribitol phosphate) teichoic acid biosynthetic process / isoprenoid biosynthetic process / cell wall organization
Similarity search - Function
Ribitol-5-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ribitol-5-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.772 Å
AuthorsYang, C.S. / Chen, S.C. / Chen, Y.R. / Kuan, S.M. / Liu, Y.H. / Chen, Y.
CitationJournal: To be Published
Title: Crystal structure of ribitol 5-phosphate cytidylyltransferase (TarI) from Bacillus subtilis
Authors: Yang, C.S. / Chen, S.C. / Chen, Y.R. / Kuan, S.M. / Liu, Y.H. / Chen, Y.
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ribitol-5-phosphate cytidylyltransferase
B: ribitol-5-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)56,2832
Polymers56,2832
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-21 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.747, 60.977, 91.808
Angle α, β, γ (deg.)90.00, 113.44, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ribitol-5-phosphate cytidylyltransferase


Mass: 28141.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria)
Strain: w23 / Gene: BSUW23_17565, ispD, tarI / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8RKI9, D-ribitol-5-phosphate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG 6000, 0.1M MES-NaOH (pH 6.0), 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.772→30 Å / Num. all: 50947 / Num. obs: 49878 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.458 / Num. unique all: 4894 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F1C

3f1c


Resolution: 1.772→24.71 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8156 / SU ML: 0.18 / σ(F): 1.37 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2534 5.08 %
Rwork0.2064 --
obs0.2082 49876 97.42 %
all-50947 -
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.25 Å2 / Biso mean: 38.96 Å2 / Biso min: 11.6 Å2
Refinement stepCycle: LAST / Resolution: 1.772→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 0 325 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083570
X-RAY DIFFRACTIONf_angle_d1.2754824
X-RAY DIFFRACTIONf_dihedral_angle_d15.0471357
X-RAY DIFFRACTIONf_chiral_restr0.088569
X-RAY DIFFRACTIONf_plane_restr0.008615
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7721-1.80610.3251180.2646233488
1.8061-1.8430.28621310.2549263197
1.843-1.8830.27051170.2545261297
1.883-1.92680.28661360.235258897
1.9268-1.9750.29541450.235260397
1.975-2.02840.28031140.237266397
2.0284-2.0880.25621370.2262262798
2.088-2.15540.26041210.2174266798
2.1554-2.23240.22881490.2137260398
2.2324-2.32170.26751480.2305263498
2.3217-2.42730.27371370.2263264498
2.4273-2.55510.2541600.2163264498
2.5551-2.7150.25081650.2229263298
2.715-2.92430.24691400.2264268899
2.9243-3.21810.22971620.2115263999
3.2181-3.68240.22291530.1875268399
3.6824-4.63440.21551540.1658272799
4.6344-24.71240.22781470.1952272398

+
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://pdbjlvh1.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