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- PDB-6xhq: Crystal structure of S. aureus TarI in complex with CDP-ribitol (... -

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Basic information

Entry
Database: PDB / ID: 6xhq
TitleCrystal structure of S. aureus TarI in complex with CDP-ribitol (space group C121)
ComponentsRibitol-5-phosphate cytidylyltransferase 1
KeywordsTRANSFERASE / 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. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
CDP-ribitol / Ribitol-5-phosphate cytidylyltransferase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, F.K.K. / Strynadka, N.C.J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis.
Authors: Li, F.K.K. / Gale, R.T. / Petrotchenko, E.V. / Borchers, C.H. / Brown, E.D. / Strynadka, N.C.J.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribitol-5-phosphate cytidylyltransferase 1
B: Ribitol-5-phosphate cytidylyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3394
Polymers58,2642
Non-polymers1,0752
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-17 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.935, 40.057, 91.823
Angle α, β, γ (deg.)90.000, 109.260, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 11 or resid 19...
21(chain B and (resid 1 through 21 or (resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILE(chain A and (resid 1 through 11 or resid 19...AA1 - 111 - 11
12PROPROGLUGLU(chain A and (resid 1 through 11 or resid 19...AA19 - 4719 - 47
13LYSLYSLYSLYS(chain A and (resid 1 through 11 or resid 19...AA4848
14METMETASPASP(chain A and (resid 1 through 11 or resid 19...AA1 - 2371 - 237
15METMETASPASP(chain A and (resid 1 through 11 or resid 19...AA1 - 2371 - 237
16METMETASPASP(chain A and (resid 1 through 11 or resid 19...AA1 - 2371 - 237
17METMETASPASP(chain A and (resid 1 through 11 or resid 19...AA1 - 2371 - 237
21METMETPROPRO(chain B and (resid 1 through 21 or (resid 22...BB1 - 211 - 21
22LYSLYSLYSLYS(chain B and (resid 1 through 21 or (resid 22...BB2222
23METMETILEILE(chain B and (resid 1 through 21 or (resid 22...BB1 - 2351 - 235

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Components

#1: Protein Ribitol-5-phosphate cytidylyltransferase 1


Mass: 29132.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tarI, SAOUHSC_00225 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G1C0, D-ribitol-5-phosphate cytidylyltransferase
#2: Chemical ChemComp-V2V / CDP-ribitol / [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate


Mass: 537.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M MIB buffer, pH 9, 25% PEG1500, 5 mM CDP-ribitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→47.475 Å / Num. obs: 20322 / % possible obs: 99.26 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rpim(I) all: 0.06798 / Net I/σ(I): 8.45
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 2022 / CC1/2: 0.609 / Rpim(I) all: 0.6366 / % possible all: 98.83

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JIS

4jis


Resolution: 2.4→47.475 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1017 5.01 %
Rwork0.1941 19293 -
obs0.1948 20310 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.1 Å2 / Biso mean: 58.1624 Å2 / Biso min: 25.19 Å2
Refinement stepCycle: final / Resolution: 2.4→47.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 68 132 3817
Biso mean--43.38 47.16 -
Num. residues----465
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1370X-RAY DIFFRACTION5.254TORSIONAL
12B1370X-RAY DIFFRACTION5.254TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.52660.3261420.3024268999
2.5266-2.68480.38731440.2839272699
2.6848-2.89210.33711440.2697272899
2.8921-3.18310.26181450.23252755100
3.1831-3.64360.24871440.194274499
3.6436-4.58990.19311460.1547277499
4.5899-47.4750.19891520.1532877100
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)
11.5635-0.4426-1.55682.4999-2.34524.76270.16330.1581.51710.8931-0.15340.2733-0.96450.6780.09610.5308-0.015-0.08140.45510.01011.0037-26.031114.14112.5988
27.18861.3785-1.47991.4902-2.15617.82050.20130.29130.8438-0.2109-0.2661-0.2735-0.4550.21450.07190.49210.0520.01080.31330.00250.5734-22.19397.93344.3068
33.1144-0.90370.24711.5557-0.64063.0647-0.0248-0.1412-0.0475-0.040.07960.26760.0956-0.0574-0.04650.3760.0219-0.01090.2777-0.04020.4911-31.17993.815813.3411
44.602-1.5711-0.06031.7183-0.52442.6425-0.3069-1.0248-0.16170.28290.29680.06280.08810.12070.01130.39030.06110.01030.41120.01180.452-25.6281-1.113426.6629
57.56991.37831.80029.77123.6092.4906-0.39770.37450.6069-0.76220.44010.11160.24440.71520.13890.4352-0.00570.04760.5460.09590.6033-10.61712.68847.1606
69.1384-0.0132.42254.2592-2.77263.576-0.1395-0.5094-0.1597-0.42870.23-0.21440.76790.5348-0.17010.41920.21420.09550.6738-0.04390.51117.9216-9.655117.7972
75.5156-0.7411-0.22322.9627-1.02173.0838-0.1153-1.16970.04450.1550.1351-0.52780.25061.1823-0.06920.4670.18580.02611.1077-0.05310.719214.0365-10.510423.7278
82.0369-1.301-0.62411.7796-0.17082.2312-0.3356-1.29180.17060.49410.3947-0.41610.12590.8219-0.06890.5030.2041-0.07790.9498-0.07320.5574-2.3606-2.72732.365
93.708-1.7734-1.08233.0663-0.16986.49090.0459-0.5739-0.02850.14060.30110.11150.320.4803-0.33630.32530.1221-0.01580.701-0.01410.5102-3.2039-5.167526.631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )A1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 41 )A22 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 150 )A42 - 150
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 220 )A151 - 220
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 237 )A221 - 237
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 31 )B1 - 31
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 99 )B32 - 99
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 183 )B100 - 183
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 235 )B184 - 235

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