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- PDB-6xhp: Crystal structure of S. aureus TarI (space group C121) -

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Basic information

Entry
Database: PDB / ID: 6xhp
TitleCrystal structure of S. aureus TarI (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
Ribitol-5-phosphate cytidylyltransferase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)58,4593
Polymers58,2642
Non-polymers1941
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-5 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.960, 37.905, 87.507
Angle α, β, γ (deg.)90.000, 115.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 9 or (resid 20...
21(chain B and (resid 2 through 148 or (resid 149...

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
11LYSLYSGLYGLY(chain A and (resid 2 through 9 or (resid 20...AA2 - 92 - 9
12LEULEULEULEU(chain A and (resid 2 through 9 or (resid 20...AA2020
13METMETGLYGLY(chain A and (resid 2 through 9 or (resid 20...AA1 - 2331 - 233
14METMETGLYGLY(chain A and (resid 2 through 9 or (resid 20...AA1 - 2331 - 233
15METMETGLYGLY(chain A and (resid 2 through 9 or (resid 20...AA1 - 2331 - 233
16METMETGLYGLY(chain A and (resid 2 through 9 or (resid 20...AA1 - 2331 - 233
21LYSLYSSERSER(chain B and (resid 2 through 148 or (resid 149...BB2 - 1482 - 148
22LYSLYSLYSLYS(chain B and (resid 2 through 148 or (resid 149...BB149149
23LYSLYSARGARG(chain B and (resid 2 through 148 or (resid 149...BB2 - 2322 - 232
24LYSLYSARGARG(chain B and (resid 2 through 148 or (resid 149...BB2 - 2322 - 232
25LYSLYSARGARG(chain B and (resid 2 through 148 or (resid 149...BB2 - 2322 - 232
26LYSLYSARGARG(chain B and (resid 2 through 148 or (resid 149...BB2 - 2322 - 232

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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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M MIB buffer, pH 9, 25% PEG1500

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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: 1.9→42.95 Å / Num. obs: 34543 / % possible obs: 99.4 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rpim(I) all: 0.0518 / Net I/σ(I): 9.14
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 3 % / Num. unique obs: 3387 / CC1/2: 0.593 / Rpim(I) all: 0.6185 / % possible all: 99.06

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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: 1.9→42.95 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 1727 5 %
Rwork0.1918 32799 -
obs0.1937 34526 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.9 Å2 / Biso mean: 51.9472 Å2 / Biso min: 18.56 Å2
Refinement stepCycle: final / Resolution: 1.9→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 13 179 3655
Biso mean--64.8 46.36 -
Num. residues----447
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1326X-RAY DIFFRACTION2.886TORSIONAL
12B1326X-RAY DIFFRACTION2.886TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.95590.32531400.3143266999
1.9559-2.0190.34741420.27852704100
2.019-2.09120.28011440.2593272199
2.0912-2.17490.2751430.22972727100
2.1749-2.27390.28281420.22512704100
2.2739-2.39380.27621430.2175271199
2.3938-2.54380.2631450.2072740100
2.5438-2.74010.23951430.19772729100
2.7401-3.01580.27381440.2019272799
3.0158-3.4520.26731460.1957276599
3.452-4.34860.18481440.1627274599
4.3486-42.950.18061510.1575285799
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)
18.04143.4089-1.42585.905-1.10254.5263-0.0591-0.10610.75020.0139-0.0432-0.3287-0.25170.75520.08010.20550.0364-0.08280.28630.05640.3131-23.23979.32277.334
21.8670.34850.13312.5909-1.02472.036-0.00890.00210.16610.15350.02670.0332-0.059-0.1646-0.04430.20770.0012-0.02580.1896-0.00720.2418-32.05939.68347.8518
33.8477-0.43510.89030.9636-0.70352.97240.0913-0.2657-0.05120.0028-0.00370.04870.14920.0086-0.08410.2410.0008-0.02490.1611-0.03230.2384-26.6359-4.352617.1063
47.11230.63484.41471.92170.35253.52110.6099-0.8515-0.58750.203-0.0767-0.14550.25350.3264-0.61420.3491-0.0292-0.02810.56160.02660.3581-12.8692-5.461728.8509
52.6905-0.97720.99346.47034.04773.6698-0.2609-0.8160.1960.99050.14680.56140.2945-0.73820.2670.3630.040.05290.42960.02990.2891-37.7221.143623.8699
66.05511.77063.15376.20163.292.8114-0.5029-1.08041.21740.35790.2443-0.3899-0.908-0.04450.25080.7250.0749-0.13380.7397-0.1690.6291-30.24224.772630.9622
79.37992.8297-3.35733.609-4.02318.28630.1443-0.6582-0.03390.164-0.12820.00140.1929-0.0652-0.04530.20010.0226-0.08590.2134-0.03670.2421-22.4758-4.277418.626
84.60684.47964.5984.40344.42824.6336-0.1771.64390.77830.01540.3656-0.44770.41971.794-0.27580.40280.0352-0.04280.67270.11080.5266-9.69532.78225.5561
94.855-1.9913-1.25932.57260.52383.15220.1230.2519-0.1328-0.0259-0.2008-0.10950.70861.71940.0250.43720.299-0.00671.29680.09120.402513.983-10.852418.5892
102.5321-0.761-0.2181.6642-0.81982.74240.09-0.66590.280.1124-0.0742-0.1832-0.06970.6897-0.00540.3142-0.0367-0.06610.5899-0.0480.2534-2.2016-2.226428.2632
117.2891-4.77220.88047.00820.73853.9716-0.2144-0.3572-1.21010.72550.11150.8082.02771.6343-0.00090.88190.22260.03410.93150.12440.4243.6139-13.204436.9427
124.7194-0.82510.36371.70030.38965.02560.18530.34250.15020.009-0.0899-0.06850.27280.1953-0.07540.2349-0.0243-0.03180.44420.02410.268-2.0504-2.791218.4557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )A1 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 99 )A32 - 99
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 150 )A100 - 150
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 169 )A151 - 169
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 182 )A170 - 182
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 201 )A183 - 201
7X-RAY DIFFRACTION7chain 'A' and (resid 202 through 220 )A202 - 220
8X-RAY DIFFRACTION8chain 'A' and (resid 221 through 233 )A221 - 233
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 99 )B2 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 169 )B100 - 169
11X-RAY DIFFRACTION11chain 'B' and (resid 170 through 202 )B170 - 202
12X-RAY DIFFRACTION12chain 'B' and (resid 203 through 232 )B203 - 232

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