PDB-9ras: Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione

ID or keywords:

Entry

Database: PDB / ID: 9ras

Title

Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione

Components

NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

Keywords

OXIDOREDUCTASE / GapN / Soaking / Fragment screening

Function / homology

Function and homology information

glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function

Biological species

Streptococcus pyogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.57 Å

Authors

Wirsing, R. / Schindelin, H.

Funding support

1items

Citation

Journal: To Be Published
Title: Streptococcus pyogenes GapN in complex with imidazoline-2,4-dione
Authors: Wirsing, R. / Schindelin, H.

History

Deposition	May 21, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ras.cif.gz	2.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9ras.ent.gz		Display	PDB format
PDBx/mmJSON format	9ras.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ra/9ras ftp://data.pdbj.org/pub/pdb/validation_reports/ra/9ras	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (7) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (7)

Deposited unit

A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

428 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
214 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

hetero molecules

defined by author&software
214 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.153, 97.154, 100.702
Angle α, β, γ (deg.)	76.94, 77.99, 68.28
Int Tables number	1
Space group name H-M	P1
Symmetry operation	#1: x,y,z

#1: Protein	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase Mass: 52959.152 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: E0F67_08075 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4U9C786
#2: Chemical	... ChemComp-A1JDZ / 1~{H}-imidazole-2,4-diol Mass: 100.076 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C₃H₄N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4556 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.01 Å³/Da / Density % sol: 38.84 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop Details: BisTris buffer pH 6.7 Li2SO4 polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 14, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.57→46.58 Å / Num. obs: 430858 / % possible obs: 82.24 % / Redundancy: 3.7 % / B_iso Wilson estimate: 15.41 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.06996 / R_pim(I) all: 0.04199 / R_rim(I) all: 0.08173 / Net I/σ(I): 12.46
Reflection shell	Resolution: 1.57→1.626 Å / R_merge(I) obs: 0.8566 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7656 / CC_1/2: 0.599 / R_pim(I) all: 0.5044 / R_rim(I) all: 0.9949

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.57→46.58 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1912	19204	5.06 %
R_work	0.1548	-	-
obs	0.1567	379285	81.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.57→46.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28432	0	224	4556	33212

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	30579
X-RAY DIFFRACTION	f_angle_d	0.744	41802
X-RAY DIFFRACTION	f_dihedral_angle_d	12.596	11420
X-RAY DIFFRACTION	f_chiral_restr	0.048	4896
X-RAY DIFFRACTION	f_plane_restr	0.007	5442

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.57-1.58	0.2508	22	0.2422	640	X-RAY DIFFRACTION	4
1.58-1.6	0.2994	113	0.2148	1985	X-RAY DIFFRACTION	14
1.6-1.62	0.2693	169	0.2174	3671	X-RAY DIFFRACTION	25
1.62-1.64	0.2755	332	0.2197	5634	X-RAY DIFFRACTION	39
1.64-1.66	0.2959	453	0.2171	8391	X-RAY DIFFRACTION	57
1.66-1.69	0.252	595	0.2148	10976	X-RAY DIFFRACTION	75
1.69-1.71	0.2558	720	0.2248	12853	X-RAY DIFFRACTION	87
1.71-1.74	0.2549	775	0.2227	13674	X-RAY DIFFRACTION	93
1.74-1.76	0.2519	686	0.2121	13901	X-RAY DIFFRACTION	94
1.76-1.79	0.2612	731	0.2074	13737	X-RAY DIFFRACTION	94
1.79-1.82	0.2514	765	0.2049	13725	X-RAY DIFFRACTION	93
1.82-1.86	0.2338	720	0.1927	13617	X-RAY DIFFRACTION	93
1.86-1.89	0.2375	758	0.1924	13514	X-RAY DIFFRACTION	92
1.89-1.93	0.237	725	0.1876	12991	X-RAY DIFFRACTION	89
1.93-1.97	0.2218	719	0.1713	12980	X-RAY DIFFRACTION	88
1.97-2.02	0.212	795	0.1627	14082	X-RAY DIFFRACTION	96
2.02-2.07	0.1992	787	0.1645	14029	X-RAY DIFFRACTION	96
2.07-2.12	0.2025	740	0.1549	14002	X-RAY DIFFRACTION	96
2.12-2.19	0.1988	719	0.1511	14119	X-RAY DIFFRACTION	96
2.19-2.26	0.1892	709	0.1432	14077	X-RAY DIFFRACTION	95
2.26-2.34	0.1863	758	0.1436	13940	X-RAY DIFFRACTION	95
2.34-2.43	0.185	675	0.1445	13965	X-RAY DIFFRACTION	94
2.43-2.54	0.192	745	0.1441	13752	X-RAY DIFFRACTION	94
2.54-2.68	0.1882	657	0.1511	13509	X-RAY DIFFRACTION	91
2.68-2.84	0.1867	652	0.1567	12639	X-RAY DIFFRACTION	86
2.84-3.06	0.1865	756	0.149	14073	X-RAY DIFFRACTION	96
3.06-3.37	0.1751	716	0.1504	14164	X-RAY DIFFRACTION	96
3.37-3.86	0.1622	736	0.1266	13969	X-RAY DIFFRACTION	95
3.86-4.86	0.1378	689	0.1141	13650	X-RAY DIFFRACTION	93
4.86-46.58	0.1607	787	0.1491	13822	X-RAY DIFFRACTION	94

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.1791	0.0915	-0.0231	0.0562	-0.0143	0.0692	-0.0392	0.0441	0.0591	-0.0471	0.0264	-0.0143	0.0189	-0.0066	-0.0305	0.0906	-0.0084	0.0139	0.0893	0.0034	0.0911	40.9983	-34.0339	-9.416
2	0.0921	-0.0052	-0.0439	0.0421	-0.059	0.1628	-0.0373	-0.0408	0.2706	-0.0194	-0.0132	0.1402	0.0053	0.0206	-0.1055	-0.1098	-0.0062	-0.0274	0.0772	-0.0462	0.3331	43.5616	-7.393	14.4363
3	0.1034	0.0117	-0.0347	0.0235	-0.0291	0.0411	-0.0076	-0.0348	-0.0029	-0.0037	-0.0005	-0.0048	-0.0015	0.0051	-0.0289	0.0402	0.0022	-0.0002	0.0754	-0.0064	0.0818	2.9283	-35.4376	16.4936
4	0.0807	0.0617	-0.0157	0.0637	0.0234	0.0491	-0.0235	-0.0949	0.0167	0.0445	-0.0144	-0.0411	0.0028	0.0544	-0.0683	0.0779	0.0366	0.0016	0.1886	0.0112	0.1011	29.8796	-45.0178	37.7687
5	0.0471	0.0257	-0.0615	0.0214	-0.0138	0.0723	0.0557	-0.0007	0.0348	-0.0194	-0.0022	-0.022	-0.0958	-0.1404	0.0353	0.1977	0.0267	0.0061	0.1703	0.0071	0.0867	-25.2835	8.385	-13.0828
6	0.0309	0.0552	-0.0337	0.0738	-0.0936	0.0767	-0.028	0.0113	-0.0031	-0.0392	0.0494	0.01	0.0073	-0.003	0.0664	0.1518	-0.0248	-0.013	0.0687	0.0022	0.0567	-17.0722	-21.7236	-29.8699
7	0.0973	0.0266	-0.0233	0.1079	-0.046	0.0375	0.0076	0.0088	-0.006	0.0591	0.003	0.0064	-0.0249	-0.0106	0.0299	0.1071	0.0022	0.0066	0.0669	0.0003	0.0545	-9.0348	19.4564	-55.1861
8	0.0695	-0.0113	-0.098	0.0696	-0.0064	0.107	0.0105	-0.0877	-0.0556	0.0488	-0.0011	-0.0397	-0.0153	0.0738	-0.0009	0.1474	-0.0087	-0.0238	0.1477	0.0199	0.1053	17.4027	7.394	-35.7772

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 2 through 475)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 2 through 475)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 2 through 475)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 1 through 475)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 2 through 475)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 2 through 475)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 2 through 475)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid -11 through 502)

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