PDB-9csz: Crystallographic structure of M271 a new Kunitz-STI from potato

ID or keywords:

Entry

Database: PDB / ID: 9csz

Title

Crystallographic structure of M271 a new Kunitz-STI from potato

Components

KTI-A protein

Keywords

PLANT PROTEIN / Kunitz / Serine Proteases / Serine Proteinase Inhibitors / Soybean Trypsin Inhibitor / Trypsin Inhibitor

Function / homology

Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / serine-type endopeptidase inhibitor activity / Chem-ETE / alpha-D-mannopyranose / KTI-A protein

Function and homology information

Biological species

Solanum tuberosum (potato)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Campuzano-Gonzalez, A. / Rudino-Pinera, E.

Funding support

United States, 2items

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural determination of a new non-canonical inhibition complex between porcine trypsin and M271 a potato Kunitz-STI inhibitor.
Authors: Campuzano-Gonzalez, A. / Gil-Rodriguez, P. / Quintana-Armas, A.X. / Guerra, Y. / Perez, Y. / Rudino-Pinera, E.

History

Deposition	Jul 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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

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Related structure data

Related structure data	9ct1C C: citing same article (ref.)
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	#247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #74 - Feb 2006 alpha-Amylase similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

B: KTI-A protein

A: KTI-A protein

hetero molecules

44.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	62.398, 76.711, 82.369
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein

KTI-A protein

Mass: 21727.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: obtained from genomic DNA sequencing from Solanum tuberosum (potato) samples isolated with the plant CTAB method
Source: (gene. exp.)

Solanum tuberosum (potato) / Gene: KTI-A / Plasmid: pPICZaC / Production host:

Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: A0A097H115

#2: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃

#3: Chemical

ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₂₀O₅

#4: Sugar

ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

Has protein modification

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: 2.35 Å³/Da / Density % sol: 47.61 %
Crystal grow	Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.08 M Tris-HCl pH 8.5, 0.2 M magnesium chloride, 24% w/v PEG 4000, and 20% v/v glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2018
Radiation	Monochromator: Si (111) Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97919 Å / Relative weight: 1
Reflection	Resolution: 1.65→49.74 Å / Num. obs: 48325 / % possible obs: 100 % / Redundancy: 9.4 % / CC_1/2: 0.99 / Net I/σ(I): 14.7
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2359 / CC_1/2: 0.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
Aimless	0.7.9	data scaling
iMOSFLM	7.0.3	data reduction
PHASER	2.7.17	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→49.74 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2028	2212	4.92 %
R_work	0.1747	-	-
obs	0.1762	44987	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→49.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3000	0	79	283	3362

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3333
X-RAY DIFFRACTION	f_angle_d	0.871	4537
X-RAY DIFFRACTION	f_dihedral_angle_d	8.897	2977
X-RAY DIFFRACTION	f_chiral_restr	0.059	484
X-RAY DIFFRACTION	f_plane_restr	0.006	593

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 (%)
1.69-1.7267	0.2868	143	0.228	2628	X-RAY DIFFRACTION	100
1.7267-1.7669	0.2318	143	0.2064	2623	X-RAY DIFFRACTION	100
1.7669-1.8111	0.2016	132	0.1907	2645	X-RAY DIFFRACTION	100
1.8111-1.8601	0.218	129	0.1855	2634	X-RAY DIFFRACTION	100
1.8601-1.9148	0.2264	145	0.1782	2653	X-RAY DIFFRACTION	100
1.9148-1.9766	0.2176	122	0.1747	2654	X-RAY DIFFRACTION	100
1.9766-2.0473	0.2203	126	0.1676	2659	X-RAY DIFFRACTION	100
2.0473-2.1292	0.1768	129	0.167	2650	X-RAY DIFFRACTION	100
2.1292-2.2261	0.2043	118	0.1691	2673	X-RAY DIFFRACTION	100
2.2261-2.3435	0.2194	115	0.1752	2687	X-RAY DIFFRACTION	100
2.3435-2.4903	0.2075	110	0.1821	2701	X-RAY DIFFRACTION	100
2.4903-2.6825	0.2252	163	0.1878	2651	X-RAY DIFFRACTION	100
2.6825-2.9524	0.2188	133	0.1868	2697	X-RAY DIFFRACTION	100
2.9524-3.3795	0.2072	181	0.1707	2642	X-RAY DIFFRACTION	100
3.3795-4.2571	0.1871	170	0.1504	2716	X-RAY DIFFRACTION	100
4.2571-41.7458	0.163	153	0.1721	2862	X-RAY DIFFRACTION	100

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	1.8278	-0.2221	-0.3688	1.7529	0.3147	2.3548	0.039	0.1175	0.0761	-0.1065	0.0161	-0.1469	-0.0905	0.1228	-0.086	0.0752	-0.0235	-0.0075	0.1102	-0.0045	0.0864	-9.4486	16.0029	-36.0239
2	1.676	1.6785	-1.2273	1.6925	-1.3451	2.0528	0.022	0.1647	0.1851	0.1243	-0.0482	0.6287	-0.1149	-0.4332	-0.0805	0.1305	0.0319	0.0402	0.5013	0.0454	0.4917	-31.3287	10.9071	-20.2176
3	1.0847	0.0457	0.1971	0.8748	0.2461	0.9199	0.0104	0.0083	-0.0476	-0.0097	0.0311	0.0318	0.0152	-0.0082	-0.0449	0.0751	-0.0055	-0.0084	0.0737	0.0018	0.0972	-18.5845	8.0395	-32.936
4	2.0128	0.981	0.1074	4.8724	-0.1715	2.2515	0.0039	-0.0395	0.2081	-0.3416	-0.1456	0.0184	-0.034	-0.1883	0.076	0.2408	-0.0205	0.019	0.2401	-0.0072	0.2076	-27.5639	-4.6356	-48.6297
5	2.0419	-0.4248	0.7321	4.6927	1.8954	2.6788	0.0006	-0.0458	-0.0049	-0.1217	-0.0689	0.1439	-0.2246	-0.2533	0.0424	0.0822	0.0119	-0.0019	0.0917	0.0139	0.0968	-26.5598	15.8072	-35.2933
6	3.7519	0.0319	1.4715	2.6828	-0.1719	3.8852	-0.1607	0.1596	0.2691	0.0862	-0.002	-0.1785	-0.1358	0.4228	0.1423	0.0936	-0.0108	0.028	0.069	-0.0263	0.0722	-9.5199	16.6271	-34.1568
7	3.1138	-0.624	1.342	1.821	-0.0025	3.7231	0.1599	-0.3352	-0.285	0.3778	-0.0431	-0.0924	0.2974	0.1151	-0.1514	0.1873	-0.0162	-0.0356	0.1531	0.0343	0.1317	-5.869	10.3583	-1.4907
8	3.8611	0.6777	-0.389	2.9594	0.2181	3.6595	0.2416	0.0313	0.5617	0.0028	-0.1115	0.7644	-0.4312	-0.4157	-0.1611	0.1637	0.0426	0.0018	0.1497	-0.0394	0.2258	-16.7278	25.7004	-15.4378
9	1.7379	0.1185	0.1923	1.7673	0.2156	2.7193	0.0193	-0.0195	0.0602	0.055	-0.0309	-0.0513	-0.1529	0.1728	0.0069	0.1052	-0.0077	-0.0116	0.0721	-0.0076	0.0726	-6.2594	20.6856	-12.8757
10	2.4714	-1.854	-1.7465	4.5712	4.3186	4.0794	-0.1431	0.0625	0.6545	-0.2162	-0.09	0.316	-0.629	-0.3296	0.1953	0.6764	0.1359	0.0745	0.1845	0.0629	0.4642	-13.653	41.225	-8.0953
11	1.2159	0.1348	0.4709	1.5854	0.5656	1.9145	0.0337	-0.1843	0.19	0.204	-0.041	-0.0796	-0.4151	0.2243	0.0278	0.2274	-0.0534	-0.0205	0.162	-0.0151	0.1201	-2.6708	27.6357	-2.7165
12	1.1235	0.1894	0.8795	0.2307	-0.0104	0.8147	-0.105	-0.3912	-0.0347	0.2146	0.0499	-0.245	-0.2883	0.5114	0.0158	1.0123	0.1201	-0.3066	0.9303	-0.0427	0.7501	6.6654	34.0685	8.4875
13	2.3085	-0.0913	0.341	2.9835	0.3517	2.519	0.035	-0.1033	0.1106	0.0634	-0.1166	0.214	-0.2207	-0.0933	0.0899	0.0882	-0.0072	0.0073	0.1129	-0.0134	0.071	-13.5097	21.9716	-7.7372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	Chain A and resid 4:40
2	X-RAY DIFFRACTION	2	Chain A and resid 41:45
3	X-RAY DIFFRACTION	3	Chain A and resid 46:146
4	X-RAY DIFFRACTION	4	Chain A and resid 147:159
5	X-RAY DIFFRACTION	5	Chain A and resid 160:178
6	X-RAY DIFFRACTION	6	Chain A and resid 179:194
7	X-RAY DIFFRACTION	7	Chain B and resid 2:27
8	X-RAY DIFFRACTION	8	Chain B and resid 28:46
9	X-RAY DIFFRACTION	9	Chain B and resid 47:103
10	X-RAY DIFFRACTION	10	Chain B and resid 104:110
11	X-RAY DIFFRACTION	11	Chain B and resid 111:151
12	X-RAY DIFFRACTION	12	Chain B and resid 152:158
13	X-RAY DIFFRACTION	13	Chain B and resid 159:194

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