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- PDB-4wpg: Group A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose... -

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Basic information

Entry
Database: PDB / ID: 4wpg
TitleGroup A Streptococcus GacA is an essential dTDP-4-dehydrorhamnose reductase (RmlD)
ComponentsdTDP-4-dehydrorhamnose reductase
KeywordsOXIDOREDUCTASE / RmlD / dTDP-4-dehydrorhamnose reductase
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / : / dTDP-rhamnose biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / dTDP-4-dehydrorhamnose reductase / :
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
Authorsvan der Beek, S.L. / Le Breton, Y. / Ferenbach, A.T. / van Aalten, D.M.F. / Navratilova, I. / McIver, K. / van Sorge, N.M. / Dorfmueller, H.C.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: GacA is essential for Group A Streptococcus and defines a new class of monomeric dTDP-4-dehydrorhamnose reductases (RmlD).
Authors: van der Beek, S.L. / Le Breton, Y. / Ferenbach, A.T. / Chapman, R.N. / van Aalten, D.M. / Navratilova, I. / Boons, G.J. / McIver, K.S. / van Sorge, N.M. / Dorfmueller, H.C.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8674
Polymers32,5361
Non-polymers3313
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-16 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.482, 45.977, 48.867
Angle α, β, γ (deg.)66.30, 81.21, 95.27
Int Tables number1
Space group name H-MP1

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Components

#1: Protein dTDP-4-dehydrorhamnose reductase


Mass: 32535.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: GacA / Plasmid: pGEXHIS6 / Details (production host): His6GST / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: T0BV37, UniProt: Q9A0G6*PLUS, dTDP-4-dehydrorhamnose reductase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.45 % / Description: bar
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M ...Details: PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M of each carboxylic acid (0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 0.2 M sodium oxamate) and 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.89 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.1→43.8 Å / Num. obs: 108172 / % possible obs: 94.03 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Net I/σ(I): 22.5
Reflection shellResolution: 1.1→1.14 Å / Mean I/σ(I) obs: 5.7 / % possible all: 85.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
Cootmodel building
PHENIXphasing
RefinementResolution: 1.1→43.77 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.031 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15494 5445 5 %RANDOM
Rwork0.1289 ---
obs0.1302 102724 94.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.021 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20.29 Å2-0.07 Å2
2--0.59 Å2-0.51 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.1→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 21 468 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192391
X-RAY DIFFRACTIONr_bond_other_d0.0020.022204
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.9473263
X-RAY DIFFRACTIONr_angle_other_deg1.52935064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63824.957117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0871510
X-RAY DIFFRACTIONr_chiral_restr0.2750.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022763
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4790.781177
X-RAY DIFFRACTIONr_mcbond_other1.4460.7781176
X-RAY DIFFRACTIONr_mcangle_it1.7131.1751480
X-RAY DIFFRACTIONr_mcangle_other1.741.1771481
X-RAY DIFFRACTIONr_scbond_it1.9840.9751214
X-RAY DIFFRACTIONr_scbond_other1.980.971211
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2741.3951778
X-RAY DIFFRACTIONr_long_range_B_refined2.3649.25511312
X-RAY DIFFRACTIONr_long_range_B_other2.2278.20510704
X-RAY DIFFRACTIONr_rigid_bond_restr10.22234595
X-RAY DIFFRACTIONr_sphericity_free11.602525
X-RAY DIFFRACTIONr_sphericity_bonded6.64754982
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 385 -
Rwork0.202 6940 -
obs--85.83 %
Refinement TLS params.Method: refined / Origin x: 0.6884 Å / Origin y: -0.7174 Å / Origin z: 0.3707 Å
111213212223313233
T0.0207 Å2-0.0046 Å2-0.0079 Å2-0.012 Å20.0062 Å2--0.0229 Å2
L0.519 °20.027 °2-0.0111 °2-1.2158 °2-0.5609 °2--1.6379 °2
S0.0625 Å °-0.0613 Å °0.0027 Å °0.0097 Å °-0.002 Å °-0.0512 Å °0.1305 Å °0.0273 Å °-0.0605 Å °

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