PDB-7f91: SeMet derivative of Thrombocorticin

ID or keywords:

Entry

Database: PDB / ID: 7f91

Title

SeMet derivative of Thrombocorticin

Components

Thrombocorticin

Keywords

SUGAR BINDING PROTEIN / bioactive protein / Thrombocorticin

Biological species

Corticium sp.

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.401 Å

Authors

Kageyama, H. / Onodera, K. / Sakai, R. / Tanaka, Y.

Citation

Journal: Nat Commun / Year: 2022
Title: A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation.
Authors: Watari, H. / Kageyama, H. / Masubuchi, N. / Nakajima, H. / Onodera, K. / Focia, P.J. / Oshiro, T. / Matsui, T. / Kodera, Y. / Ogawa, T. / Yokoyama, T. / Hirayama, M. / Hori, K. / Freymann, D. ...

History

Deposition	Jul 3, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2023	Group: Data collection / Database references / Category: citation / citation_author / diffrn_source Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7f91.cif.gz	63.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7f91.ent.gz	48.1 KB	Display	PDB format
PDBx/mmJSON format	7f91.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7f91_validation.pdf.gz	428 KB	Display	wwPDB validaton report
Full document	7f91_full_validation.pdf.gz	429.9 KB	Display
Data in XML	7f91_validation.xml.gz	13.8 KB	Display
Data in CIF	7f91_validation.cif.gz	20 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f9/7f91 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/7f91	HTTPS FTP

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Related structure data

Related structure data	7f9fC 7f9gC 7f9jC 7fblC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thrombocorticin

B: Thrombocorticin

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

1

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

Unit cell

Length a, b, c (Å)	41.800, 45.000, 109.910
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Thrombocorticin Mass: 14963.933 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corticium sp. (in: Fungi) (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.89 Å³/Da / Density % sol: 34.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: sodium acetate, PEG 5000, PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PHOTON FACTORY / Beamline: BL-1A / Wavelength: 0.9785 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.4→41.645 Å / Num. obs: 78682 / % possible obs: 99.9 % / Redundancy: 7.04 % / R_sym value: 0.097 / Net I/σ(I): 11.28
Reflection shell	Resolution: 1.4→1.49 Å / Num. unique obs: 12705 / R_sym value: 0.663

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.401→41.645 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 18.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2001	3940	5.01 %
R_work	0.1752	-	-
obs	0.1765	78674	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.401→41.645 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1913	0	0	247	2160

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	1976
X-RAY DIFFRACTION	f_angle_d	0.893	2696
X-RAY DIFFRACTION	f_dihedral_angle_d	16.061	709
X-RAY DIFFRACTION	f_chiral_restr	0.088	311
X-RAY DIFFRACTION	f_plane_restr	0.005	365

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 (%)
1.4011-1.4182	0.2808	138	0.2471	2644	X-RAY DIFFRACTION	99
1.4182-1.4361	0.246	140	0.2307	2699	X-RAY DIFFRACTION	100
1.4361-1.455	0.2736	140	0.2187	2639	X-RAY DIFFRACTION	100
1.455-1.4749	0.2505	139	0.2206	2612	X-RAY DIFFRACTION	100
1.4749-1.496	0.2234	146	0.2134	2767	X-RAY DIFFRACTION	100
1.496-1.5183	0.2416	137	0.2051	2610	X-RAY DIFFRACTION	100
1.5183-1.5421	0.1982	141	0.2014	2730	X-RAY DIFFRACTION	100
1.5421-1.5673	0.2955	140	0.2059	2640	X-RAY DIFFRACTION	100
1.5673-1.5944	0.2284	142	0.2011	2647	X-RAY DIFFRACTION	100
1.5944-1.6234	0.2452	141	0.1861	2669	X-RAY DIFFRACTION	100
1.6234-1.6546	0.2635	142	0.1859	2688	X-RAY DIFFRACTION	100
1.6546-1.6884	0.2068	135	0.1868	2654	X-RAY DIFFRACTION	100
1.6884-1.7251	0.22	143	0.1833	2718	X-RAY DIFFRACTION	100
1.7251-1.7652	0.2357	144	0.1817	2624	X-RAY DIFFRACTION	100
1.7652-1.8094	0.1965	142	0.1769	2671	X-RAY DIFFRACTION	100
1.8094-1.8583	0.2318	142	0.1788	2686	X-RAY DIFFRACTION	100
1.8583-1.913	0.2119	139	0.1856	2660	X-RAY DIFFRACTION	100
1.913-1.9747	0.1825	147	0.1748	2671	X-RAY DIFFRACTION	100
1.9747-2.0453	0.2136	138	0.1626	2684	X-RAY DIFFRACTION	100
2.0453-2.1272	0.1603	138	0.1611	2661	X-RAY DIFFRACTION	100
2.1272-2.224	0.1851	140	0.1596	2644	X-RAY DIFFRACTION	100
2.224-2.3412	0.1929	144	0.1714	2689	X-RAY DIFFRACTION	100
2.3412-2.4879	0.2075	141	0.187	2676	X-RAY DIFFRACTION	100
2.4879-2.6799	0.2057	137	0.1772	2671	X-RAY DIFFRACTION	100
2.6799-2.9496	0.1928	139	0.1769	2662	X-RAY DIFFRACTION	100
2.9496-3.3762	0.2449	143	0.1729	2670	X-RAY DIFFRACTION	100
3.3762-4.253	0.1516	141	0.1525	2660	X-RAY DIFFRACTION	100
4.253-41.645	0.156	141	0.1548	2688	X-RAY DIFFRACTION	100

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