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- PDB-6xh9: Crystal structure of S. aureus TarJ -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6xh9
TitleCrystal structure of S. aureus TarJ
ComponentsRibulose-5-phosphate reductase 1
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase
Function / homology
Function and homology information


ribitol-5-phosphate 2-dehydrogenase (NADP+) / ribitol-5-phosphate 2-dehydrogenase [(NAD(P)+] activity / poly(ribitol phosphate) teichoic acid biosynthetic process / cell wall organization / zinc ion binding
Similarity search - Function
Ribulose-5-phosphate reductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Ribulose-5-phosphate reductase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose-5-phosphate reductase 1


Theoretical massNumber of molelcules
Total (without water)38,5661
Polymers38,5661
Non-polymers00
Water00
1
A: Ribulose-5-phosphate reductase 1

A: Ribulose-5-phosphate reductase 1


Theoretical massNumber of molelcules
Total (without water)77,1322
Polymers77,1322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/31
Buried area1980 Å2
ΔGint-11 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.483, 99.483, 268.428
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Ribulose-5-phosphate reductase 1 / TarJ / Ribulose-5-P reductase 1 / Ribitol-5-phosphate dehydrogenase 1


Mass: 38565.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: tarJ, SAOUHSC_00226 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G1B9, ribitol-5-phosphate 2-dehydrogenase (NADP+)
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: 4.97 Å3/Da / Density % sol: 75.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 1.1 M ammonium phosphate monobasic, 0.1 M sodium citrate pH 5.6

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Oct 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.2→48.909 Å / Num. obs: 13739 / % possible obs: 99.88 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rpim(I) all: 0.05771 / Net I/σ(I): 13.44
Reflection shellResolution: 3.2→3.315 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 1340 / CC1/2: 0.698 / Rpim(I) all: 0.5733

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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: 4ILK

4ilk


Resolution: 3.2→48.909 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 687 5 %
Rwork0.2076 13045 -
obs0.2091 13732 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.46 Å2 / Biso mean: 109.3954 Å2 / Biso min: 68.24 Å2
Refinement stepCycle: final / Resolution: 3.2→48.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 0 0 2372
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012425
X-RAY DIFFRACTIONf_angle_d1.2023310
X-RAY DIFFRACTIONf_dihedral_angle_d2.861405
X-RAY DIFFRACTIONf_chiral_restr0.076387
X-RAY DIFFRACTIONf_plane_restr0.01424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2002-3.44730.29561330.28242529
3.4473-3.79410.26751330.22992529
3.7941-4.34280.24221350.18862573
4.3428-5.47030.18341380.17722609
5.4703-48.9090.25411480.21352805
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)
13.99181.4594-1.35835.4528-0.18083.2375-0.1552-0.2852-0.0953-0.0523-0.1804-0.5321-0.3796-0.48740.31150.9880.1416-0.1260.6495-0.14560.82435.80936.378811.3867
24.3067-1.36450.83224.12190.43953.34940.0750.10990.08650.13210.03510.0652-0.4987-0.4974-0.1381.19760.42360.00890.6866-0.05570.808225.112126.193532.5481
30.6433-0.5124-1.36421.20292.09835.15890.22290.3930.2866-0.28370.1537-0.3947-1.4144-0.5749-0.29971.35080.4499-0.01870.7385-0.0440.945429.759419.603619.181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 136 )A1 - 136
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 265 )A137 - 265
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 341 )A266 - 341

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