PDB-3s8k: Crystal structure of a papaya latex serine protease inhibitor (PP...

ID or keywords:

Entry

Database: PDB / ID: 3s8k

Title

Crystal structure of a papaya latex serine protease inhibitor (PPI) at 1.7A resolution

Components

Latex serine proteinase inhibitor

Keywords

HYDROLASE INHIBITOR / Kunitz-STI fold / protease inhibitor

Function / homology

Function and homology information

serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function

Biological species

Carica papaya (papaya)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Garcia-Pino, A.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: The plasticity of the beta-Trefoil fold constitutes an evolutionary platform for protease inhibition
Authors: Azarkan, M. / Martinez-Rodriguez, S. / Buts, L. / Baeyens-Volant, D. / Garcia-Pino, A.

History

Deposition	May 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2013	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3	Nov 20, 2019	Group: Data collection / Database references / Derived calculations Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif Item: _chem_comp.type / _struct_conn_type.id / _struct_ref_seq_dif.details
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Nov 20, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3s8k.cif.gz	100.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s8/3s8k ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8k	HTTPS FTP

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Related structure data

Related structure data	3s8jC C: citing same article (ref.)
Similar structure data	6bm9-2 7yas-3 6bm9-1 2p72-d 5ur5-1 1dfv-d 2bfk-d 2pbr-d 3eeb-d 2a6v-d Search similar-shape structures by Omokage search (details) 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	#135 - Mar 2011 Integrase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Latex serine proteinase inhibitor

B: Latex serine proteinase inhibitor

hetero molecules

43.7 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)	44.262, 81.992, 140.891
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein

Latex serine proteinase inhibitor

Mass: 20682.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural)

Carica papaya (papaya) / References: UniProt: P80691

#2: Polysaccharide

alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

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Non-polymers , 5 types, 427 molecules

#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H₄N
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.09 Å³/Da / Density % sol: 60.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M ammonium sulfate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.8073 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2005
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8073 Å / Relative weight: 1
Reflection	Resolution: 1.7→20 Å / Num. all: 51816 / Num. obs: 51816 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.15 % / Net I/σ(I): 17.3
Reflection shell	Resolution: 1.7→1.76 Å / % possible all: 90.5

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Processing

Software

Name	Version	Classification
MAR345		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→19.682 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1993	2632	5.08 %
R_work	0.1812	-	-
obs	0.1822	51816	90.46 %
all	-	51816	-

Solvent computation

Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.588 Å² / k_sol: 0.473 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.6296 Å²	0 Å²	-0 Å²
2-	-	19.7026 Å²	0 Å²
3-	-	-	-15.073 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→19.682 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2853	0	140	411	3404

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3103
X-RAY DIFFRACTION	f_angle_d	1.541	4220
X-RAY DIFFRACTION	f_dihedral_angle_d	12.591	1126
X-RAY DIFFRACTION	f_chiral_restr	0.092	467
X-RAY DIFFRACTION	f_plane_restr	0.006	525

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 (%)
1.7-1.7309	0.2724	119	0.2599	2307	X-RAY DIFFRACTION	83
1.7309-1.7642	0.2321	127	0.2299	2300	X-RAY DIFFRACTION	81
1.7642-1.8002	0.2661	110	0.2174	2333	X-RAY DIFFRACTION	83
1.8002-1.8393	0.2512	128	0.2153	2312	X-RAY DIFFRACTION	82
1.8393-1.882	0.2161	119	0.1992	2307	X-RAY DIFFRACTION	82
1.882-1.9291	0.1969	133	0.1895	2333	X-RAY DIFFRACTION	82
1.9291-1.9812	0.19	128	0.182	2405	X-RAY DIFFRACTION	85
1.9812-2.0394	0.2083	122	0.1687	2428	X-RAY DIFFRACTION	86
2.0394-2.1052	0.2086	142	0.1871	2619	X-RAY DIFFRACTION	92
2.1052-2.1803	0.2057	149	0.1762	2621	X-RAY DIFFRACTION	94
2.1803-2.2675	0.2069	141	0.1652	2696	X-RAY DIFFRACTION	94
2.2675-2.3705	0.1856	149	0.1644	2705	X-RAY DIFFRACTION	96
2.3705-2.4953	0.1955	155	0.1595	2780	X-RAY DIFFRACTION	97
2.4953-2.6513	0.1845	154	0.1587	2839	X-RAY DIFFRACTION	99
2.6513-2.8554	0.1779	139	0.1571	2877	X-RAY DIFFRACTION	99
2.8554-3.1417	0.1919	145	0.1635	2881	X-RAY DIFFRACTION	99
3.1417-3.5939	0.171	158	0.1677	2824	X-RAY DIFFRACTION	98
3.5939-4.5189	0.1833	154	0.1685	2769	X-RAY DIFFRACTION	94
4.5189-19.683	0.2331	160	0.231	2848	X-RAY DIFFRACTION	93

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	1.7796	-0.9606	0.2343	2.0501	0.251	1.5283	0.0784	0.0258	-0.0453	0.1219	-0.0381	-0.0132	0.1614	0.2596	-0.0194	0.2317	-0.0063	-0.0099	0.2967	0.0059	0.2225	23.0886	38.0563	27.2408
2	5.2811	-0.5253	-1.3266	3.3849	0.6835	3.8932	0.188	-0.3122	0.6042	0.3488	-0.3632	0.9331	-0.2921	-0.6725	0.1223	0.2741	0.0909	0.0388	0.7119	-0.107	0.3747	2.4739	53.0335	24.8922
3	1.0418	0.1626	0.0336	0.75	-0.2499	1.295	0.0203	0.1503	-0.1736	-0.1521	-0.0345	0.0702	0.161	0.0686	0.0059	0.2143	0.0269	-0.0084	0.2482	-0.0235	0.1916	21.497	38.8129	20.1998
4	1.2991	-0.4862	0.241	1.929	0.222	1.1777	0.1044	0.0467	0.0072	-0.1511	-0.1368	0.286	-0.0923	-0.3731	0.0167	0.2176	0.0208	-0.0068	0.3206	-0.0292	0.2224	11.4383	48.1111	18.5947
5	1.2224	-0.4238	-1.6771	0.597	0.9536	4.5588	0.0046	0.499	-0.0216	0.0309	0.0628	0.0996	0.351	-0.228	-0.1012	0.2658	0.0056	-0.0265	0.2933	-0.0213	0.2137	14.951	46.8092	10.7965
6	1.4992	-0.5824	1.9224	1.0536	-1.167	3.8378	0.0911	0.4194	0.0332	-0.0283	-0.122	-0.0642	-0.2042	0.674	0.0521	0.2593	0.0266	0.0003	0.3248	-0.0011	0.2184	25.7019	46.1788	18.3369
7	1.4515	-0.1611	0.2601	0.8844	0.1572	2.9772	0.1577	0.2037	0.145	-0.0969	-0.0783	-0.0422	-0.3785	0.2652	-0.073	0.2666	0.0165	0.0293	0.3334	0.0157	0.2411	24.676	53.6072	9.9115
8	2.2996	-0.0323	-1.5486	0.6917	0.0359	1.8181	0.2604	-0.1332	0.2229	0.0415	-0.0506	0.0285	-0.4763	-0.0506	-0.1427	0.2647	0.0125	0.0226	0.2908	-0.0014	0.2531	16.3369	55.5216	29.0821
9	3.0183	0.4945	0.2206	2.8863	-0.4875	3.0421	0.0664	-0.2157	-0.337	0.0952	-0.0438	-0.0962	0.2863	-0.0849	0.0375	0.2187	-0.0169	-0.0324	0.2774	0.0265	0.1982	23.8227	40.286	28.8999
10	1.6894	0.0473	0.5147	2.3659	-0.5183	2.0127	0.1039	-0.1994	-0.0358	-0.172	0.018	0.094	0.2409	-0.2721	-0.0737	0.2208	-0.0169	-0.0117	0.2448	0.0191	0.2275	37.8728	30.8225	43.5508
11	1.3787	-0.0134	0.4945	1.2137	0.1217	1.9991	-0.1087	0.5037	0.1728	-0.1491	0.0655	-0.0731	-0.3379	0.4709	0.0837	0.2536	-0.0721	-0.0097	0.355	0.0516	0.2196	53.0437	46.7863	42.5321
12	0.6628	0.2956	0.0036	0.6852	0.009	0.8334	0.0601	-0.0387	-0.0884	0.0915	-0.012	-0.0547	0.0352	-0.1444	-0.0352	0.2199	-0.0098	-0.0129	0.2599	0.033	0.2476	42.8705	33.8918	48.228
13	0.2894	0.0593	0.2663	0.9379	-0.1039	2.3548	0.0181	-0.0871	-0.0114	0.1131	0.0137	-0.0479	-0.2022	0.048	-0.0282	0.1783	0.0009	-0.0028	0.2411	0.0031	0.1838	45.5283	41.2339	55.4892
14	1.6043	0.5065	0.1729	1.3825	-0.0519	2.0124	0.0186	0.1	0.1726	0.0534	0.0487	0.0184	-0.3225	0.0224	-0.0545	0.2549	0.0135	-0.0036	0.2401	0.0109	0.2211	44.605	47.8164	44.6716

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 2:37)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 38:47)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 48:78)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 79:106)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 107:118)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 119:140)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 141:154)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 155:171)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 172:184)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 2:24)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 25:47)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 48:78)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 79:154)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 155:183)

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