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- PDB-9g4o: The strucuture of Streptococcus pyogenes GacA in complex with a f... -

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Basic information

Entry
Database: PDB / ID: 9g4o
TitleThe strucuture of Streptococcus pyogenes GacA in complex with a fragment
ComponentsdTDP-4-dehydrorhamnose reductase
KeywordsOXIDOREDUCTASE / GacA / Streptococcus / fragment
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsYan, K. / Dorfmueller, H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust225350/Z/22/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
CitationJournal: To Be Published
Title: Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Raimi, O. / Kowalski, B. / Gurvic, D. / Grillenberger, S. / Chen, X. / Ferenbach, A.T. / Dorfmueller, H. / van Aalten, D.M.F.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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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)33,6015
Polymers32,5361
Non-polymers1,0664
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-27 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.155, 45.702, 48.440
Angle α, β, γ (deg.)113.30, 99.54, 95.01
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: rmlD, SPy_0784 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9A0G6, dTDP-4-dehydrorhamnose reductase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-A1IH7 / 2-[4-(hydroxymethyl)phenyl]ethanoic acid


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M 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: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M 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), 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.545→43.411 Å / Num. obs: 21968 / % possible obs: 79.8 % / Redundancy: 3.1 % / CC1/2: 0.934 / Net I/σ(I): 5.4
Reflection shellResolution: 1.545→1.81 Å / Num. unique obs: 1098 / CC1/2: 0.547

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→43.41 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 1148 5.15 %
Rwork0.1818 --
obs0.1842 21968 54.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 72 163 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082418
X-RAY DIFFRACTIONf_angle_d0.9953301
X-RAY DIFFRACTIONf_dihedral_angle_d11.297330
X-RAY DIFFRACTIONf_chiral_restr0.053362
X-RAY DIFFRACTIONf_plane_restr0.007420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.620.147560.228943X-RAY DIFFRACTION1
1.62-1.70.2472170.2615252X-RAY DIFFRACTION5
1.7-1.810.2429390.248744X-RAY DIFFRACTION15
1.81-1.950.31591170.23832166X-RAY DIFFRACTION45
1.95-2.140.28061840.2084195X-RAY DIFFRACTION86
2.14-2.450.25192310.19134579X-RAY DIFFRACTION95
2.45-3.090.22712690.18644630X-RAY DIFFRACTION96
3.09-43.410.19212850.15124534X-RAY DIFFRACTION95

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