PDB-7qe9: Human cationic trypsin (TRY1) complexed with serine protease inhi...

ID or keywords:

Entry

Database: PDB / ID: 7qe9

Title

Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 N34S (SPINK1 N34S)

Components

Serine protease inhibitor Kazal-type 1
Trypsin-1

Keywords

HYDROLASE / TRY1 / SPINK1 / serine protease / protease-inhibitor complex / catalytic triad

Function / homology

Function and homology information

negative regulation of nitric oxide mediated signal transduction / Uptake of dietary cobalamins into enterocytes / regulation of acrosome reaction / positive regulation of pancreatic juice secretion / regulation of store-operated calcium entry / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of calcium ion import / cellular response to peptide hormone stimulus / sperm capacitation / endopeptidase inhibitor activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Nagel, F. / Palm, G.J. / Delcea, M. / Lammers, M.

Funding support

European Union, 2items

Citation

Journal: Int J Mol Sci / Year: 2022
Title: Structural and Biophysical Insights into SPINK1 Bound to Human Cationic Trypsin.
Authors: Nagel, F. / Palm, G.J. / Geist, N. / McDonnell, T.C.R. / Susemihl, A. / Girbardt, B. / Mayerle, J. / Lerch, M.M. / Lammers, M. / Delcea, M.

History

Deposition	Dec 1, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 30, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 27, 2022	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	May 1, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7qe9.cif.gz	393.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7qe9_validation.pdf.gz	459.5 KB	Display	wwPDB validaton report
Full document	7qe9_full_validation.pdf.gz	464.2 KB	Display
Data in XML	7qe9_validation.xml.gz	23.9 KB	Display
Data in CIF	7qe9_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qe/7qe9 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/7qe9	HTTPS FTP

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Related structure data

Related structure data	7qe8C 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	#46 - Oct 2003 Trypsin similarity (8) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #53 - May 2004 Serpins similarity (1)

Deposited unit

A: Trypsin-1

B: Trypsin-1

D: Serine protease inhibitor Kazal-type 1

C: Serine protease inhibitor Kazal-type 1

hetero molecules

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

1

A: Trypsin-1

C: Serine protease inhibitor Kazal-type 1

hetero molecules

defined by author&software
Evidence: gel filtration
31.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Trypsin-1

D: Serine protease inhibitor Kazal-type 1

hetero molecules

defined by author&software
Evidence: gel filtration
30.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	76.555, 76.555, 189.719
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Trypsin-1 / Beta-trypsin / Cationic trypsinogen / Serine protease 1 / Trypsin I Mass: 24121.201 Da / Num. of mol.: 2 / Mutation: S200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / References: UniProt: P07477, trypsin
#2: Protein	Serine protease inhibitor Kazal-type 1 / Pancreatic secretory trypsin inhibitor / Tumor-associated trypsin inhibitor / TATI Mass: 6714.578 Da / Num. of mol.: 2 / Mutation: N34S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPINK1, PSTI / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / References: UniProt: P00995
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.71 Å³/Da / Density % sol: 54.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1 uL protein solution (20 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl) + 1 uL well solution (15% PEG 4000, 0.3 M AS), cryo: 15% PEG 4000, 0.3 M AS, 8% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Oct 23, 2020 / Details: DCM Si(111)
Radiation	Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 38593 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 19.7 % / B_iso Wilson estimate: 50.1 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.179 / R_sym value: 0.174 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.1→2.22 Å / Redundancy: 19.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6081 / CC_1/2: 0.411 / R_rim(I) all: 3.256 / R_sym value: 3.172 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	VERSION Feb 5, 2021	data reduction
XDS	VERSION Feb 5, 2021	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TRN_A, 1CGI_I

Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.947 / SU B: 12.904 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.202 / ESU R Free: 0.175
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2336	1899	4.93 %
R_work	0.1927	36619	-
all	0.195	-	-
obs	-	38518	99.974 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 50.032 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.174 Å²	0.087 Å²	-0 Å²
2-	-	0.174 Å²	0 Å²
3-	-	-	-0.565 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4241	0	20	231	4492

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	4371
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	4029
X-RAY DIFFRACTION	r_angle_refined_deg	1.838	1.641	5943
X-RAY DIFFRACTION	r_angle_other_deg	1.354	1.582	9307
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.786	5	564
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.453	23.932	206
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.006	15	712
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.506	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	568
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5100
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	984
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	882
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	3775
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	2099
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	2207
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	254
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.011	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.266	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.226	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.226	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	1.889	3.252	2253
X-RAY DIFFRACTION	r_mcbond_other	1.889	3.252	2252
X-RAY DIFFRACTION	r_mcangle_it	2.727	4.875	2812
X-RAY DIFFRACTION	r_mcangle_other	2.727	4.875	2813
X-RAY DIFFRACTION	r_scbond_it	2.548	3.532	2118
X-RAY DIFFRACTION	r_scbond_other	2.52	3.522	2113
X-RAY DIFFRACTION	r_scangle_it	3.804	5.192	3129
X-RAY DIFFRACTION	r_scangle_other	3.759	5.178	3123
X-RAY DIFFRACTION	r_lrange_it	6.422	39.64	4867
X-RAY DIFFRACTION	r_lrange_other	6.402	39.354	4829

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 (%)
2.1-2.154	0.417	134	0.328	2666	X-RAY DIFFRACTION	99.9643
2.154-2.213	0.345	115	0.303	2596	X-RAY DIFFRACTION	100
2.213-2.277	0.241	153	0.282	2511	X-RAY DIFFRACTION	100
2.277-2.347	0.329	135	0.255	2442	X-RAY DIFFRACTION	99.9612
2.347-2.424	0.284	143	0.224	2337	X-RAY DIFFRACTION	100
2.424-2.509	0.239	117	0.21	2336	X-RAY DIFFRACTION	99.9593
2.509-2.603	0.236	100	0.199	2231	X-RAY DIFFRACTION	100
2.603-2.709	0.27	114	0.192	2153	X-RAY DIFFRACTION	100
2.709-2.83	0.253	111	0.203	2086	X-RAY DIFFRACTION	100
2.83-2.967	0.263	92	0.191	1970	X-RAY DIFFRACTION	100
2.967-3.127	0.247	102	0.194	1877	X-RAY DIFFRACTION	100
3.127-3.316	0.22	72	0.215	1838	X-RAY DIFFRACTION	100
3.316-3.544	0.255	92	0.202	1662	X-RAY DIFFRACTION	99.943
3.544-3.826	0.229	87	0.167	1591	X-RAY DIFFRACTION	100
3.826-4.189	0.211	68	0.147	1461	X-RAY DIFFRACTION	100
4.189-4.679	0.173	85	0.134	1320	X-RAY DIFFRACTION	100
4.679-5.395	0.161	68	0.14	1186	X-RAY DIFFRACTION	100
5.395-6.589	0.288	53	0.182	1022	X-RAY DIFFRACTION	100
6.589-9.238	0.172	36	0.188	822	X-RAY DIFFRACTION	100
9.238-50	0.269	22	0.277	508	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	2.5755	0.689	0.2405	1.6262	0.4415	2.382	0.0208	0.1695	-0.1351	-0.0453	-0.0307	0.0195	0.1955	-0.001	0.0099	0.0968	0.016	-0.0065	0.1017	-0.0113	0.0095	-15.429	11.7948	5.6317
2	2.9102	0.6882	-0.2009	1.7735	0.057	2.9438	0.0697	0.0013	-0.0648	0.1472	-0.0496	-0.3111	-0.2233	0.4866	-0.0201	0.1491	-0.0539	-0.0062	0.2197	0.0108	0.0589	13.5869	29.0061	24.0259
3	2.391	-0.0513	1.784	5.311	-2.4773	7.3711	0.104	0.2835	0.5466	-0.1958	-0.1438	-0.2415	-0.5267	0.5662	0.0398	0.3363	-0.0762	0.0959	0.3009	0.034	0.2851	17.559	44.6134	8.1575
4	6.1401	-0.3086	2.9408	0.6301	0.1716	3.0075	0.0468	0.3657	0.518	-0.1596	-0.0088	-0.0492	-0.2851	0.0164	-0.038	0.2017	-0.0001	0.0117	0.1588	0.0068	0.1466	-36.4115	13.7209	-6.2302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	24 - 247
2	X-RAY DIFFRACTION	2	ALL	B	24 - 247
3	X-RAY DIFFRACTION	3	ALL	D	26 - 79
4	X-RAY DIFFRACTION	4	ALL	C	20 - 79

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