PDB-8r28: Crystal structure of Amacstatin-1, a cystatin from the hard tick ...

ID or keywords:

Entry

Database: PDB / ID: 8r28

Title

Crystal structure of Amacstatin-1, a cystatin from the hard tick Amblyomma maculatum

Components

Cystatin domain-containing protein

Keywords

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

MOLECULAR REPLACEMENT / Resolution: 1.807 Å

Authors

Busa, M. / Mares, M.

Funding support

Czech Republic, 1items

Citation

Journal: To Be Published
Title: Crystal structure of Amacstatin-1, 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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Download

PDBx/mmCIF format	8r28.cif.gz	59 KB	Display	PDBx/mmCIF format
PDB format	pdb8r28.ent.gz	40.1 KB	Display	PDB format
PDBx/mmJSON format	8r28.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8r28_validation.pdf.gz	430.7 KB	Display	wwPDB validaton report
Full document	8r28_full_validation.pdf.gz	430.7 KB	Display
Data in XML	8r28_validation.xml.gz	8.9 KB	Display
Data in CIF	8r28_validation.cif.gz	11.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/8r28 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r28	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

hetero molecules

13.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	98.411, 98.411, 27.579
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Cystatin domain-containing protein Mass: 13388.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amblyomma maculatum (Gulf Coast tick) / Production host: Komagataella pastoris (fungus) / References: UniProt: G3MPE6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.28 Å³/Da / Density % sol: 62.53 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M ammonium phosphate, 0.1 M Tris-HCl pH 8.5, 50% (v/v) MPD Temp details: AC room

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
Detector	Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 16, 2020
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54187 Å / Relative weight: 1
Reflection	Resolution: 1.807→42.61 Å / Num. obs: 13304 / % possible obs: 92.1 % / Redundancy: 4.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.068 / Net I/σ(I): 80.7
Reflection shell	Resolution: 1.807→1.84 Å / Redundancy: 1.3 % / R_merge(I) obs: 0.129 / Num. unique obs: 183 / CC_1/2: 0.965 / R_rim(I) all: 0.177 / % possible all: 21.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.807→28.425 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.941 / SU B: 2.598 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2023	686	5.201 %
R_work	0.161	12504	-
all	0.163	-	-
obs	-	13190	91.737 %

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: 21.061 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.769 Å²	0.384 Å²	0 Å²
2-	-	0.769 Å²	-0 Å²
3-	-	-	-2.493 Å²

Refinement step

Cycle: LAST / Resolution: 1.807→28.425 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	817	0	5	141	963

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	852
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	777
X-RAY DIFFRACTION	r_angle_refined_deg	1.51	1.675	1161
X-RAY DIFFRACTION	r_angle_other_deg	0.508	1.575	1801
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.826	5	106
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.996	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.428	10	148
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.724	10	41
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	136
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	982
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	188
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	141
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.205	0.2	651
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	412
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	458
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	95
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.146	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.136	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.122	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	2.314	2.15	415
X-RAY DIFFRACTION	r_mcbond_other	2.185	2.136	414
X-RAY DIFFRACTION	r_mcangle_it	3.331	3.829	518
X-RAY DIFFRACTION	r_mcangle_other	3.361	3.835	519
X-RAY DIFFRACTION	r_scbond_it	3.469	2.512	437
X-RAY DIFFRACTION	r_scbond_other	3.404	2.492	434
X-RAY DIFFRACTION	r_scangle_it	5.18	4.431	641
X-RAY DIFFRACTION	r_scangle_other	5.092	4.393	636
X-RAY DIFFRACTION	r_lrange_it	6.936	25.428	986
X-RAY DIFFRACTION	r_lrange_other	6.718	23.101	944

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
1.807-1.854	0.323	12	0.278	263	0.28	1072	0.809	0.932	25.653	0.244
1.854-1.904	0.358	36	0.269	716	0.273	986	0.915	0.944	76.2677	0.247
1.904-1.959	0.244	36	0.221	966	0.221	1010	0.952	0.963	99.2079	0.185
1.959-2.019	0.264	53	0.189	908	0.193	962	0.958	0.973	99.896	0.156
2.019-2.085	0.2	42	0.175	896	0.176	942	0.977	0.98	99.5754	0.152
2.085-2.158	0.201	46	0.156	837	0.158	885	0.968	0.983	99.774	0.137
2.158-2.239	0.174	44	0.15	842	0.151	886	0.976	0.985	100	0.127
2.239-2.33	0.181	45	0.146	794	0.148	840	0.977	0.986	99.881	0.124
2.33-2.432	0.174	40	0.151	769	0.152	813	0.984	0.985	99.508	0.128
2.432-2.55	0.23	49	0.158	718	0.163	780	0.97	0.984	98.3333	0.135
2.55-2.687	0.191	46	0.17	685	0.172	740	0.973	0.981	98.7838	0.148
2.687-2.848	0.195	38	0.172	655	0.174	694	0.977	0.981	99.8559	0.152
2.848-3.043	0.172	33	0.167	634	0.167	671	0.979	0.982	99.4039	0.15
3.043-3.283	0.269	43	0.161	557	0.168	620	0.96	0.985	96.7742	0.153
3.283-3.592	0.176	20	0.15	528	0.151	557	0.986	0.989	98.3842	0.148
3.592-4.008	0.147	36	0.142	477	0.142	534	0.989	0.988	96.0674	0.142
4.008-4.613	0.137	33	0.109	411	0.111	470	0.987	0.993	94.4681	0.118
4.613-5.613	0.206	16	0.128	367	0.131	393	0.988	0.992	97.4555	0.138
5.613-7.787	0.288	10	0.184	299	0.186	315	0.961	0.981	98.0952	0.182
7.787-28.425	0.347	8	0.18	182	0.187	203	0.9	0.977	93.5961	0.205

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