PDB-8r29: Crystal structure of domain swapped dimer of Amacstatin-2, a cyst...

ID or keywords:

Entry

Database: PDB / ID: 8r29

Title

Crystal structure of domain swapped dimer of Amacstatin-2, a cystatin from the hard tick Amblyomma maculatum

Components

Cystatin domain-containing protein

Keywords

PROTEIN BINDING / cystatin / tick / Amblyomma maculatum / protein inhibitor / protease inhibitor

Function / homology

Function and homology information

cysteine-type endopeptidase inhibitor activity / vesicle / extracellular space / cytoplasm
Similarity search - Function

Biological species

Amblyomma maculatum (Gulf Coast tick)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.146 Å

Authors

Busa, M. / Mares, M.

Funding support

Czech Republic, 1items

Citation

Journal: To Be Published
Title: Crystal structure of domain swapped dimer of Amacstatin-2, a cystatin from the hard tick amblyomma maculatum
Authors: Busa, M. / Mares, M.

History

Deposition	Nov 3, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 13, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r29.cif.gz	211.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8r29.ent.gz	131.9 KB	Display	PDB format
PDBx/mmJSON format	8r29.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8r29_validation.pdf.gz	432.7 KB	Display	wwPDB validaton report
Full document	8r29_full_validation.pdf.gz	435 KB	Display
Data in XML	8r29_validation.xml.gz	10.9 KB	Display
Data in CIF	8r29_validation.cif.gz	13.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/8r29 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r29	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
Related items in Molecule of the Month	#224 - Aug 2018 Legumain similarity (5)

Deposited unit

A: Cystatin domain-containing protein

B: Cystatin domain-containing protein

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

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	49.172, 49.172, 86.458
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 112 / Label seq-ID: 7 - 113

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Cystatin domain-containing protein Mass: 13253.845 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MEETPRLVGGWQKKPVDGNQLFTELAHFAVGNQVGDREFFDTVLEVIDAETQVVAGTNYRLTFKIAESTCRVTETYTKELCLPKTQDVKDTCTAVIYDVPWLNQRSVSSFTCGVNAAST- Source: (gene. exp.) Amblyomma maculatum (Gulf Coast tick) / Production host: Komagataella pastoris (fungus) / References: UniProt: G3MQC0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O
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: 2.05 Å³/Da / Density % sol: 40.01 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M bicine-Tris-HCl pH 8.5, 12.5% w/v PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, and 0.3 M pentaethyleneglycol Temp details: AC room

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2019
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.146→49.172 Å / Num. obs: 10697 / % possible obs: 92.28 % / Redundancy: 6.8 % / B_iso Wilson estimate: 44.96 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.04719 / R_rim(I) all: 0.1256 / Net I/σ(I): 10.34
Reflection shell	Resolution: 2.146→2.227 Å / Redundancy: 4.1 % / R_merge(I) obs: 5.08 / Num. unique obs: 694 / CC_1/2: 0.396 / R_pim(I) all: 2.766 / R_rim(I) all: 5.828 / % possible all: 61.42

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.146→49.172 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.925 / WR_factor R_free: 0.262 / WR_factor R_work: 0.217 / SU B: 21.962 / SU ML: 0.245 / Average fsc free: 0.9286 / Average fsc work: 0.9534 / Cross valid method: FREE R-VALUE / ESU R: 0.349 / ESU R Free: 0.249
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2746	520	5.007 %	Random selection
R_work	0.2257	9865	-	-
all	0.228	-	-	-
obs	-	10385	92.155 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.6 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 49.134 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.617 Å²	-0 Å²	0 Å²
2-	-	0.617 Å²	0 Å²
3-	-	-	-1.235 Å²

Refinement step

Cycle: LAST / Resolution: 2.146→49.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1613	0	0	3	1616

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.011	1647
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1500
X-RAY DIFFRACTION	r_angle_refined_deg	1.62	1.653	2256
X-RAY DIFFRACTION	r_angle_other_deg	0.535	1.57	3421
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.781	5	217
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.698	5	5
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.874	10	234
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.978	10	60
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	277
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1946
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	378
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	238
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	1316
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	817
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	916
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.321	0.2	27
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.048	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.031	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	5.205	4.028	873
X-RAY DIFFRACTION	r_mcbond_other	5.202	4.034	874
X-RAY DIFFRACTION	r_mcangle_it	7.429	7.215	1088
X-RAY DIFFRACTION	r_mcangle_other	7.426	7.222	1089
X-RAY DIFFRACTION	r_scbond_it	5.687	4.199	774
X-RAY DIFFRACTION	r_scbond_other	5.683	4.206	775
X-RAY DIFFRACTION	r_scangle_it	8.3	7.578	1168
X-RAY DIFFRACTION	r_scangle_other	8.296	7.583	1169
X-RAY DIFFRACTION	r_lrange_it	10.269	37.374	1650
X-RAY DIFFRACTION	r_lrange_other	10.266	37.397	1651
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.147	0.05	2632

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.14708	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.14708	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.146-2.202	0.47	29	0.425	553	0.427	809	0.864	0.871	71.9407	0.425
2.202-2.262	0.649	17	0.506	324	0.513	815	0.653	0.814	41.8405	0.544
2.262-2.328	0.395	33	0.337	610	0.34	803	0.929	0.929	80.0747	0.348
2.328-2.399	0.402	36	0.317	700	0.321	755	0.901	0.933	97.4834	0.307
2.399-2.478	0.366	38	0.299	705	0.302	744	0.904	0.944	99.8656	0.282
2.478-2.564	0.377	35	0.249	673	0.256	709	0.925	0.96	99.859	0.225
2.564-2.661	0.259	34	0.234	642	0.235	676	0.964	0.967	100	0.203
2.661-2.769	0.278	34	0.232	654	0.235	688	0.955	0.966	100	0.202
2.769-2.892	0.284	32	0.231	609	0.234	641	0.934	0.966	100	0.2
2.892-3.033	0.323	30	0.219	571	0.224	601	0.934	0.969	100	0.194
3.033-3.196	0.27	29	0.215	550	0.218	579	0.948	0.972	100	0.195
3.196-3.389	0.328	28	0.198	518	0.204	546	0.935	0.979	100	0.184
3.389-3.622	0.246	26	0.204	499	0.206	526	0.963	0.981	99.8099	0.196
3.622-3.91	0.221	24	0.186	453	0.188	477	0.976	0.982	100	0.181
3.91-4.281	0.245	22	0.179	426	0.183	448	0.965	0.983	100	0.181
4.281-4.781	0.163	20	0.162	389	0.162	409	0.984	0.983	100	0.171
4.781-5.512	0.285	19	0.196	347	0.2	367	0.957	0.978	99.7275	0.208
5.512-6.73	0.34	14	0.258	273	0.262	287	0.934	0.969	100	0.272
6.73-9.43	0.19	13	0.251	236	0.247	249	0.981	0.97	100	0.288
9.43-49.172	0.293	7	0.292	133	0.292	140	0.962	0.94	100	0.353

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	1.5959	-0.2078	0.6922	0.2001	0.0459	0.4294	-0.0135	0.1288	-0.1425	0.0697	0.0742	0.0518	0.0033	0.146	-0.0607	0.1379	0.009	0.0487	0.0735	-0.0057	0.0405	22.0077	24.6684	-0.7811
2	0.8479	0.3766	0.531	0.2956	0.2946	0.3693	-0.0226	0.08	-0.039	0.116	0.1075	-0.0675	0.0577	0.0752	-0.0849	0.114	0.0709	-0.0601	0.0946	-0.0063	0.063	25.3898	23.505	-0.5387

Refinement TLS group

Selection: ALL

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