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- PDB-6xhk: Crystal structure of S. aureus TarJ in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 6xhk
TitleCrystal structure of S. aureus TarJ in complex with NADPH
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
Chem-NDP / Ribulose-5-phosphate reductase 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3112
Polymers38,5661
Non-polymers7451
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-3 kcal/mol
Surface area14050 Å2
Unit cell
Length a, b, c (Å)99.237, 99.237, 268.757
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 / 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 (strain NCTC 8325) (bacteria)
Strain: NCTC 8325 / Gene: tarJ, SAOUHSC_00226 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G1B9, ribitol-5-phosphate 2-dehydrogenase (NADP+)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
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: 4.95 Å3/Da / Density % sol: 75.17 %
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, 5 mM NADPH

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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 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3→48.794 Å / Num. obs: 16503 / % possible obs: 99.84 % / Redundancy: 18.9 % / CC1/2: 0.998 / Rpim(I) all: 0.0437 / Net I/σ(I): 17.22
Reflection shellResolution: 3→3.107 Å / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1613 / CC1/2: 0.576 / Rpim(I) all: 0.7654 / % possible all: 99.94

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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→48.794 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 825 5 %
Rwork0.2051 15668 -
obs0.2079 16493 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 199.82 Å2 / Biso mean: 105.8811 Å2 / Biso min: 64.85 Å2
Refinement stepCycle: final / Resolution: 3→48.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 48 0 2450
Biso mean--116.21 --
Num. residues----317
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0001-3.1880.44291330.36032535
3.188-3.43410.35181340.25672541
3.4341-3.77950.27791340.22182545
3.7795-4.32620.24041370.18312597
4.3262-5.44930.22251380.16912622
5.4493-48.7940.25181490.20342828
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)
12.25972.1783-0.3292.14240.01331.9751-0.1326-0.4201-0.21820.0148-0.1469-0.6455-0.0843-0.0715-0.03041.13850.2256-0.17830.858-0.15531.211940.93918.089812.0063
22.29760.529-1.2153.2382-0.03011.6021-0.12650.0755-0.31090.19920.04430.137-0.0811-0.69590.00091.07370.1674-0.00081.105-0.20510.945528.07185.130212.1231
33.0343-0.92661.13385.44390.96113.4490.09980.1909-0.06450.101-0.09760.2178-0.3461-0.50850.00441.3380.4664-0.03440.8654-0.04810.828723.71927.011131.7835
40.8387-0.2002-0.66961.39171.73844.73170.02790.23570.0817-0.24220.2327-0.1993-0.4805-0.4066-0.00341.23550.407-0.00520.8044-0.01350.978730.188320.198923.2284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 73 )A1 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 140 )A74 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 245 )A141 - 245
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 341 )A246 - 341

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