PDB-2r9y: Structure of antiplasmin

ID or keywords:

Entry

Database: PDB / ID: 2r9y

Title

Structure of antiplasmin

Components

Alpha-2-antiplasmin

Keywords

HYDROLASE INHIBITOR / alpha2-antiplasmin / inhibitory serpin / plasmin inhibitor /

Acute phase /

Glycoprotein /

Protease inhibitor /

Secreted /

Serine protease inhibitor /

Sulfation /

TOXIN

Function / homology

Function and homology information

Dissolution of Fibrin Clot / maintenance of blood vessel diameter homeostasis by renin-angiotensin / positive regulation of transforming growth factor beta production / Platelet degranulation /

fibrinogen complex / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / collagen fibril organization / blood vessel morphogenesis / positive regulation of collagen biosynthetic process ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Law, R.H.P. / Sofian, T. / Kan, W.T. / Horvath, A.J. / Hitchen, C.R. / Langendorf, C.G. / Buckle, A.M. / Whisstock, J.C. / Coughlin, P.B.

Citation

Journal: Blood / Year: 2008
Title: X-ray crystal structure of the fibrinolysis inhibitor {alpha}2-antiplasmin
Authors: Law, R.H.P. / Sofian, T. / Kan, W.T. / Horvath, A.J. / Hitchen, C.R. / Langendorf, C.G. / Buckle, A.M. / Whisstock, J.C. / Coughlin, P.B.

History

Deposition	Sep 14, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Dec 18, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Oct 25, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r9y.cif.gz	89.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2r9y.ent.gz	67.1 KB	Display	PDB format
PDBx/mmJSON format	2r9y.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/r9/2r9y ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9y	HTTPS FTP

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Related structure data

Related structure data	1hp7S 1iz2S 1qmnS 1yxaS S: Starting model for refinement
Similar structure data	3dru-3 6z1q-2 3q02-1 1lq8-2 2xn7-d 6f4u-d 6ssv-d 4dte-2 6hge-3 3dru-1 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	#53 - May 2004 Serpins similarity (9) #126 - Jun 2010 Epidermal Growth Factor similarity (1)

Deposited unit

A: Alpha-2-antiplasmin

48.6 kDa, 1 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)	115.679, 115.679, 100.533
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Alpha-2-antiplasmin / Alpha-2-plasmin inhibitor / Alpha-2-PI / Alpha-2-AP Mass: 48611.160 Da / Num. of mol.: 1 Fragment: Serpin domain plus C-terminus, UNP Residues 71-491 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Serpinf2, Pli / Plasmid: PET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q61247
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Alpha-2-antiplasmin / Alpha-2-plasmin inhibitor / Alpha-2-PI / Alpha-2-AP

Mass: 48611.160 Da / Num. of mol.: 1
Fragment: Serpin domain plus C-terminus, UNP Residues 71-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Serpinf2, Pli / Plasmid: PET-3a / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q61247

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.99 Å³/Da / Density % sol: 69.21 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 20% PEG 3350, O.2M MgSO4, 3% sucrose, 1.2% inositol, or 3% trehalose, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 5, 2006 / Details: osmic mirror
Radiation	Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.65→44.95 Å / Num. obs: 22284 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / R_merge(I) obs: 0.147 / R_sym value: 0.059 / Net I/σ(I): 15.4
Reflection shell	Highest resolution: 2.65 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.903 / Mean I/σ(I) obs: 2.1 / R_sym value: 0.381 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CrystalClear		data collection
MOSFLM		data reduction
SCALA		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 1IZ2, 1HP7, 1YXA, 1QMN

Resolution: 2.65→44.95 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.921 / SU B: 15.637 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21798	1139	5.1 %	RANDOM
R_work	0.1843	-	-	-
obs	0.18605	21122	99.87 %	-
all	-	22284	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 22.436 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.21 Å²	1.1 Å²	0 Å²
2-	-	2.21 Å²	0 Å²
3-	-	-	-3.31 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→44.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2834	0	0	82	2916

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	2922
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.949	3992
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.755	5	365
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.973	24.24	125
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.598	15	455
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.955	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	464
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2213
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	1232
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	1970
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	140
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.199	0.2	25
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	6
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.119	3	1873
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.091	5	2959
X-RAY DIFFRACTION	r_scbond_it	3.243	7	1178
X-RAY DIFFRACTION	r_scangle_it	4.943	10	1032
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	75	-
R_work	0.297	1556	-
obs	-	-	99.57 %

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	118.8176	19.0961	7.102	46.8417	0.853	22.9841	-1.1924	-5.5036	-0.8834	2.8982	1.8645	2.5119	0.789	-2.0108	-0.6721	0.3627	0.1617	0.4083	0.4847	0.4325	0.3007	43.514	3.213	12.91
2	6.2905	-0.6408	-1.441	3.8908	1.3606	1.2157	-0.1202	-0.2834	0.1659	0.2242	0.1204	-0.4881	-0.3095	0.2629	-0.0001	0.1181	-0.0161	-0.0167	0.0171	0.0422	0.2772	54.73	7.614	0.444
3	0.7632	1.0767	0.49	10.2902	-0.5977	0.5039	-0.038	0.062	-0.1641	-0.5704	0.2132	0.0335	0.1712	-0.0485	-0.1752	0.2621	-0.005	0.0569	0.0406	-0.013	0.1932	52.181	0.619	-5.383
4	7.401	-2.3141	2.3843	7.7533	-3.6692	4.8003	0.0283	-0.6298	-0.7652	0.3124	0.397	0.7911	0.5651	-0.6732	-0.4253	0.1452	-0.1379	0.0446	-0.0558	0.0212	0.2067	43.95	-0.659	4.026
5	0.8656	-1.4523	0.6244	19.1446	6.9974	8.6935	0.2578	-0.239	-0.1512	-1.0883	0.1665	0.9214	0.4127	-0.8282	-0.4242	0.0146	-0.1471	-0.1405	-0.0557	0.079	0.2728	38.088	2.376	-9.664
6	4.2944	1.02	2.2162	16.4993	0.8331	9.6	0.2105	0.0566	-0.3185	-1.4654	-0.0266	1.9885	0.9749	-1.1812	-0.1839	0.2061	-0.1235	-0.3773	-0.0936	-0.0037	0.4192	37.075	-9.801	-11.408
7	12.7882	0.0012	8.6298	17.3992	-7.4391	9.0049	0.814	0.6357	1.2903	-2.7248	-0.2097	0.3646	0.6378	-0.2294	-0.6043	0.5132	-0.0613	-0.5053	0.0486	-0.0629	0.2094	39.581	3.684	-21.807
8	0.383	-1.4976	0.3635	12.1268	1.4101	1.6239	0.1939	-0.1922	-0.1574	-1.2567	0.1987	0.5159	0.0549	-0.3372	-0.3926	0.1156	-0.0248	-0.0356	0.0718	0.0223	0.2593	41.565	13.899	-9.362
9	16.8916	-3.5098	-9.4837	2.0564	1.5143	5.9396	0.3369	-0.0183	1.0254	-0.3556	-0.0101	-0.106	-0.4403	0.1064	-0.3268	0.1343	0.0599	0.0004	-0.0014	0.001	0.2431	54.329	35.086	-14.556
10	2.3964	-0.255	0.5414	1.6011	-0.9495	5.4394	-0.0353	-0.0481	0.0543	0.1939	0.1577	0.0856	-0.1178	0.0457	-0.1224	0.104	0.0633	0.0257	0.0435	-0.0437	0.2233	49.302	29.376	1.439
11	8.9742	5.1574	-1.8682	7.6733	-2.1424	5.8362	-0.0919	-0.3602	0.231	-0.3942	-0.1437	-0.2044	-0.2914	0.5932	0.2356	0.1462	0.0699	0.0127	0.0862	0.016	0.1684	56.657	25.45	-2.627
12	11.8008	0.4043	-5.6324	10.4448	-1.6974	15.7845	0.1314	-0.9418	-0.6206	0.5887	-0.2878	-0.322	0.5602	0.8894	0.1564	0.0303	-0.0206	-0.092	-0.1164	0.0157	0.1288	57.558	18.588	4.027
13	4.4655	0.0088	-1.6228	14.7362	-13.7111	35.4336	-0.023	-0.5961	0.2924	1.0526	0.1895	0.4949	-1.9651	-0.2966	-0.1665	0.0203	0.0999	0.0284	-0.0027	-0.04	0.1316	47.137	35.098	5.611
14	5.9038	-14.3622	-2.3591	51.5604	10.5783	7.0281	0.5984	0.4468	-0.1981	-2.3977	-0.417	0.2532	0.1299	-0.206	-0.1814	0.081	0.026	0.0283	0.102	0.0198	0.07	48.152	19.574	-13.972
15	1.7893	-0.1174	-0.985	15.9965	0.7516	3.9901	0.2754	0.2404	-0.3042	-1.4473	-0.1637	-1.3256	0.2736	0.0571	-0.1117	0.2919	0.0677	0.0126	-0.1174	0.0259	0.1403	55.87	-6.437	-9.408
16	1.9817	-5.5545	-0.4494	20.2433	-0.3168	2.8575	0.2273	0.0088	-0.036	-0.9914	-0.0115	0.2999	0.6798	0.0319	-0.2158	0.236	-0.027	-0.1708	0.0384	0.0333	0.1757	46.972	-0.077	-12.968
17	5.9573	1.8888	3.805	5.1056	1.4044	9.7529	0.0857	-0.9221	0.4972	0.0953	-0.0137	0.8328	-0.7148	-0.6996	-0.072	0.042	0.0829	0.0517	0.0209	0.0569	0.2855	44.475	35.361	-0.98
18	8.9141	2.5714	-5.3965	2.4617	-3.6345	5.7772	0.0679	-0.0828	0.0299	0.2274	0.3381	0.0109	0.0794	-0.1739	-0.406	0.2028	0.0328	0.0212	0.0832	-0.0227	0.2333	51.25	20.994	-2.099
19	4.4599	0.2458	-1.1967	4.9214	-5.0207	9.4861	-0.0434	-0.4137	-0.4988	-0.2998	-0.1633	0.1457	0.7247	0.4099	0.2067	0.2157	0.07	-0.0112	0.0313	-0.0226	0.2011	49.609	15.592	-2.118
20	19.3365	6.9614	-3.2519	6.2265	-7.6042	13.2642	0.126	0.4626	1.1776	0.5761	0.287	1.1188	0	0	-0.4129	0.0846	0.0941	0.0014	0.0228	-0.0255	0.1206	57.675	32.241	-20.268

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	47 - 54
2	X-RAY DIFFRACTION	2	A	55 - 69
3	X-RAY DIFFRACTION	3	A	70 - 109
4	X-RAY DIFFRACTION	4	A	110 - 125
5	X-RAY DIFFRACTION	5	A	126 - 144
6	X-RAY DIFFRACTION	6	A	145 - 170
7	X-RAY DIFFRACTION	7	A	171 - 198
8	X-RAY DIFFRACTION	8	A	199 - 219
9	X-RAY DIFFRACTION	9	A	220 - 237
10	X-RAY DIFFRACTION	10	A	238 - 268
11	X-RAY DIFFRACTION	11	A	269 - 280
12	X-RAY DIFFRACTION	12	A	281 - 298
13	X-RAY DIFFRACTION	13	A	299 - 308
14	X-RAY DIFFRACTION	14	A	309 - 318
15	X-RAY DIFFRACTION	15	A	319 - 340
16	X-RAY DIFFRACTION	16	A	341 - 360
17	X-RAY DIFFRACTION	17	A	361 - 385
18	X-RAY DIFFRACTION	18	A	386 - 395
19	X-RAY DIFFRACTION	19	A	396 - 407
20	X-RAY DIFFRACTION	20	A	408 - 419

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