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- PDB-4jis: Crystal structure of ribitol 5-phosphate cytidylyltransferase (Ta... -

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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 / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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