PDB-8tqf: Crystal structure of Soybean SHMT8 in complex with PLP-glycine an...

ID or keywords:

Entry

Database: PDB / ID: 8tqf

Title

Crystal structure of Soybean SHMT8 in complex with PLP-glycine and diglutamylated 5-formyltetrahydrofolate

Components

Serine hydroxymethyltransferase

Keywords

TRANSFERASE / complex / enzyme / soybean

Function / homology

Function and homology information

glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.69 Å

Authors

Owuocha, L.F. / Beamer, L.J.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structural insights into high affinity binding of polyglutamylated tetrahydrofolate to soybean serine hydroxymethyltransferase
Authors: Owuocha, L.F. / Beamer, L.J.

History

Deposition	Aug 7, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tqf.cif.gz	915.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8tqf.ent.gz	629.7 KB	Display	PDB format
PDBx/mmJSON format	8tqf.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/tq/8tqf ftp://data.pdbj.org/pub/pdb/validation_reports/tq/8tqf	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

Deposited unit

A: Serine hydroxymethyltransferase

B: Serine hydroxymethyltransferase

C: Serine hydroxymethyltransferase

D: Serine hydroxymethyltransferase

hetero molecules

221 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	86.208, 89.020, 146.190
Angle α, β, γ (deg.)	90.000, 90.536, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Serine hydroxymethyltransferase Mass: 54141.355 Da / Num. of mol.: 4 Fragment: residues 71-541 (based on Uniprot numbering in A0A0R0IK90) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: 100305380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R0IK90
#2: Chemical	ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE Mass: 306.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₂O₇P
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-S8R / N-[4-({[(6R)-2-amino-5-formyl-4-hydroxy-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-glutamic acid Mass: 602.553 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₅H₃₀N₈O₁₀ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1478 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Magnesium formate dihydrate, 13% PEG 3350 0.2 M Lithium sulfate, 0.1 M Hepes pH 7.5, 25% w/v PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
Detector	Type: RDI CMOS_8M / Detector: CMOS / Date: May 28, 2023 / Details: none
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.69→47.41 Å / Num. obs: 238872 / % possible obs: 96.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 23.43 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.066 / R_pim(I) all: 0.062 / R_rim(I) all: 0.091 / Χ²: 0.88 / Net I/σ(I): 8.6
Reflection shell	Resolution: 1.69→1.72 Å / Redundancy: 2.7 % / R_merge(I) obs: 1.057 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 10106 / CC_1/2: 0.314 / R_pim(I) all: 0.975 / R_rim(I) all: 0.091 / Χ²: 0.49 / % possible all: 82.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing
Coot		model building

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.69→47.09 Å / SU ML: 0.2151 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.9366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2139	11964	5.01 %
R_work	0.1841	226747	-
obs	0.1856	238711	96.72 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 29.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.69→47.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14412	0	304	1478	16194

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	15413
X-RAY DIFFRACTION	f_angle_d	0.9956	20943
X-RAY DIFFRACTION	f_chiral_restr	0.0533	2239
X-RAY DIFFRACTION	f_plane_restr	0.0084	2746
X-RAY DIFFRACTION	f_dihedral_angle_d	9.9276	2296

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 (%)
1.69-1.71	0.3369	320	0.3089	6326	X-RAY DIFFRACTION	81.52
1.71-1.73	0.3152	352	0.2935	6757	X-RAY DIFFRACTION	86.88
1.73-1.75	0.3118	382	0.2783	7213	X-RAY DIFFRACTION	92.83
1.75-1.77	0.314	397	0.2751	7608	X-RAY DIFFRACTION	97.85
1.77-1.8	0.2887	387	0.2626	7799	X-RAY DIFFRACTION	99.3
1.8-1.82	0.2954	455	0.2492	7673	X-RAY DIFFRACTION	99.45
1.82-1.85	0.2874	403	0.2439	7760	X-RAY DIFFRACTION	99.52
1.85-1.87	0.2638	458	0.2326	7728	X-RAY DIFFRACTION	99.5
1.87-1.9	0.2783	401	0.2291	7754	X-RAY DIFFRACTION	99.6
1.9-1.93	0.2557	385	0.2166	7751	X-RAY DIFFRACTION	99.57
1.93-1.97	0.2532	412	0.215	7799	X-RAY DIFFRACTION	99.71
1.97-2	0.2711	363	0.2225	7811	X-RAY DIFFRACTION	99.68
2-2.04	0.2449	391	0.21	7746	X-RAY DIFFRACTION	99.77
2.04-2.08	0.2446	429	0.2002	7759	X-RAY DIFFRACTION	99.56
2.08-2.13	0.2394	489	0.1931	7674	X-RAY DIFFRACTION	99.68
2.13-2.18	0.2262	476	0.1926	7737	X-RAY DIFFRACTION	99.82
2.18-2.23	0.2174	414	0.1888	7741	X-RAY DIFFRACTION	99.74
2.23-2.29	0.219	395	0.1888	7801	X-RAY DIFFRACTION	99.25
2.29-2.36	0.2142	463	0.1838	7694	X-RAY DIFFRACTION	99.55
2.36-2.44	0.2251	385	0.1807	7780	X-RAY DIFFRACTION	99.19
2.44-2.52	0.2341	346	0.1825	7811	X-RAY DIFFRACTION	98.91
2.52-2.63	0.2242	421	0.1878	7648	X-RAY DIFFRACTION	97.95
2.63-2.74	0.222	392	0.1774	7603	X-RAY DIFFRACTION	97.36
2.74-2.89	0.2198	410	0.1771	7557	X-RAY DIFFRACTION	96.6
2.89-3.07	0.2026	388	0.1703	7439	X-RAY DIFFRACTION	94.92
3.07-3.31	0.1876	378	0.1675	7368	X-RAY DIFFRACTION	93.73
3.31-3.64	0.2035	346	0.1623	7303	X-RAY DIFFRACTION	92.54
3.64-4.17	0.1527	368	0.1493	7194	X-RAY DIFFRACTION	91.3
4.17-5.25	0.1654	330	0.1543	7411	X-RAY DIFFRACTION	92.96
5.25-47.09	0.1932	428	0.1808	7502	X-RAY DIFFRACTION	93.65

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	0.839571496759	0.175031035828	-0.109078833663	0.521989650111	-0.0420254641601	1.15474999483	0.0513108412375	0.0964834647845	0.0891645094211	-0.0831362211112	-0.0526123232999	0.0802001101267	-0.190339342776	-0.188496915283	-0.00230552777734	0.220904322948	0.0833495681504	-0.00916504882024	0.15905223937	0.00243407551945	0.148247962337	18.5717446758	31.3258393667	10.6747203023
2	1.13376955397	-0.009615337502	0.14572559919	0.871909738945	0.5231555144	1.55356706021	0.0175360560181	0.176436613053	-0.0182418431035	-0.145044275343	-0.132759625045	0.201714526205	-0.179541047874	-0.26738106208	0.111162689394	0.208030731994	0.0799774429389	-0.00862345368299	0.214054826641	0.00224208409657	0.178266291531	13.1558588986	28.9375738772	1.61716238352
3	1.15864631916	0.577895663764	1.15052700438	2.41002850213	2.07455652139	2.34151769103	-0.0212381300051	0.357158555644	-0.0336972402831	-0.253130036221	-0.00455326514573	0.0264088023124	-0.225080008921	0.138534568899	0.010163259581	0.339443827532	0.0951462332027	0.0172025228517	0.370443241029	-0.0376516238066	0.16436008345	23.2155666244	18.989237498	-16.7351658111
4	0.863253391842	0.127008695351	0.0333892689956	0.586062314376	-0.11633848257	0.948089782359	0.032395872	-0.0446887578797	-0.0726511333775	-0.0119187763724	-0.0428690971894	-0.0489956150642	-0.112455152374	0.0495179555949	0.00618684067888	0.156744179335	0.018384791256	0.0163731229279	0.123287637549	0.0150213972733	0.138255927251	37.0678095427	23.3905711784	18.1986426519
5	2.11166142916	-0.19734450655	0.440069731019	1.38587746366	0.855540971464	1.43498390687	0.131683915867	-0.154096960027	-0.473406645523	0.122846088499	-0.0576941947277	-0.0142593018602	0.244012742864	0.0253498875346	-0.0189003135674	0.1900021153	0.0235726945829	-0.0109271067439	0.150066677817	0.0414503573321	0.201163759037	36.8073938926	10.9013254678	17.786351356
6	1.58032370517	0.913062959505	0.455986865749	1.30794970984	0.082872636838	0.662587089874	0.0652342223533	-0.100399806276	0.287466476352	0.123948487792	-0.134700474426	0.0569755068336	-0.234202130319	0.0979441839439	0.071720696817	0.250031024373	-0.0241759360768	0.0457649603595	0.190025998991	0.00601523403366	0.188417912132	49.9687215013	39.3401454982	21.415389085
7	0.861734699944	-0.0781351321044	-0.240655411552	0.445620085016	-0.0701789830375	0.937851660692	-0.0277694213637	0.1091247144	-0.181177635559	-0.00255062222767	-0.0374032630394	0.0806003946825	0.0734384880021	-0.130033624466	0.0563430926193	0.138424833285	-0.0295451828645	0.0114401874067	0.152867076315	-0.0352756886503	0.198615230698	-2.80669221765	5.09859193763	46.1544019174
8	1.69735387552	-0.524113097005	-0.0863584031024	0.615007955331	0.0534613775196	0.537151436333	-0.0125471003902	0.0268321035835	-0.162862546373	-0.0124168115778	-0.0420810937442	0.117441576612	0.0261321742705	-0.149086035333	0.0552544607896	0.151432066392	-0.0422383355533	0.00399198377931	0.18402793735	-0.0308563728924	0.172763559616	-15.5076084956	9.73952589423	48.7492284166
9	0.969253336661	0.0746606497902	-0.0902163664289	0.570565855161	-0.222211558898	0.879684835733	-0.0517752209946	-0.0637120162653	-0.0874242353515	0.0646005800232	-0.0545310087101	-0.0547511380012	-0.0258103478124	0.142141612684	0.105865021174	0.172824865313	-0.0230555185845	0.00528048801933	0.162242452939	0.0190020947492	0.1312070842	12.6669804218	12.8736189756	58.87205192
10	2.47027031801	-0.717200917138	0.44232216074	2.19492526325	1.02865457742	1.50555678352	-0.0383206601272	0.0333545941922	0.396412625932	-0.0493548697979	-0.0555753934907	-0.10537479225	-0.383721352465	0.213620697304	0.045499257607	0.210156961656	-0.0732358574537	-0.00792856211306	0.182460564029	0.00863504505967	0.157756976199	12.4259102052	25.4496489808	58.8630410057
11	1.05502506639	-0.569580927587	0.602141006953	1.50279855053	-0.937438146798	1.08813986061	0.0858560080038	-0.000684653520196	-0.181911953381	-0.14837829446	-0.206511816189	-0.200411740843	0.27681620459	0.263479637429	0.114591496464	0.265947549996	0.0341774646612	0.0550727397393	0.270195430519	0.0801216115976	0.227471389955	21.2829809235	-3.27020087273	68.905120489

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 0 through 230 )	A	A	0 - 230	1 - 231
2	2	chain 'A' and (resid 231 through 426 )	A	A	231 - 426	232 - 427
3	3	chain 'A' and (resid 427 through 471 )	A	A	427 - 471	428 - 472
4	4	chain 'B' and (resid 0 through 230 )	B	F	0 - 230	1 - 231
5	5	chain 'B' and (resid 231 through 283 )	B	F	231 - 283	232 - 284
6	6	chain 'B' and (resid 284 through 471 )	B	F	284 - 471	285 - 472
7	7	chain 'C' and (resid 0 through 230 )	C	L	0 - 230	1 - 231
8	8	chain 'C' and (resid 231 through 471 )	C	L	231 - 471	232 - 472
9	9	chain 'D' and (resid 0 through 230 )	D	T	0 - 230	1 - 231
10	10	chain 'D' and (resid 231 through 283 )	D	T	231 - 283	232 - 284
11	11	chain 'D' and (resid 284 through 471 )	D	T	284 - 471	285 - 472

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