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- PDB-7f9f: Thrombocorticin -

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Basic information

Entry
Database: PDB / ID: 7f9f
TitleThrombocorticin
ComponentsThrombocorticin
KeywordsSUGAR BINDING PROTEIN / bioactive protein / Thrombocorticin
Biological speciesCorticium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.411 Å
AuthorsKageyama, H. / Onodera, K. / Sakai, R. / Tanaka, Y. / Freymann, D.M.
CitationJournal: 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. ...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.M. / Imai, M. / Komatsu, N. / Araki, M. / Tanaka, Y. / Sakai, R.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombocorticin
B: Thrombocorticin
C: Thrombocorticin
D: Thrombocorticin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7446
Polymers54,6954
Non-polymers492
Water14,394799
1
A: Thrombocorticin
C: Thrombocorticin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3964
Polymers27,3482
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-11 kcal/mol
Surface area10710 Å2
MethodPISA
2
B: Thrombocorticin
D: Thrombocorticin


Theoretical massNumber of molelcules
Total (without water)27,3482
Polymers27,3482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-12 kcal/mol
Surface area10780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.458, 92.445, 58.536
Angle α, β, γ (deg.)90.00, 102.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thrombocorticin


Mass: 13673.872 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Corticium sp. (in: Fungi) (fungus)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: MgCl2, Tris, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97892 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 84334 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rsym value: 0.099 / Net I/σ(I): 25.2
Reflection shellResolution: 1.41→1.43 Å / Num. unique obs: 4206 / Rsym value: 0.642

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F91

7f91


Resolution: 1.411→30.474 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 1950 2.39 %
Rwork0.1694 --
obs0.17 81705 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.411→30.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 2 799 4630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053925
X-RAY DIFFRACTIONf_angle_d0.8825358
X-RAY DIFFRACTIONf_dihedral_angle_d20.7321408
X-RAY DIFFRACTIONf_chiral_restr0.089624
X-RAY DIFFRACTIONf_plane_restr0.005722
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4113-1.44660.28911290.23735131X-RAY DIFFRACTION87
1.4466-1.48570.23311300.2185323X-RAY DIFFRACTION91
1.4857-1.52940.25741380.19965491X-RAY DIFFRACTION93
1.5294-1.57870.20311370.18465576X-RAY DIFFRACTION95
1.5787-1.63520.1951370.1775652X-RAY DIFFRACTION96
1.6352-1.70060.221420.18165706X-RAY DIFFRACTION97
1.7006-1.7780.20771370.17735703X-RAY DIFFRACTION98
1.778-1.87170.20121410.17555789X-RAY DIFFRACTION99
1.8717-1.9890.1741420.16175858X-RAY DIFFRACTION99
1.989-2.14250.19641430.16775876X-RAY DIFFRACTION100
2.1425-2.35810.19061430.16745902X-RAY DIFFRACTION100
2.3581-2.69910.18041430.18035855X-RAY DIFFRACTION100
2.6991-3.39990.19611440.16465929X-RAY DIFFRACTION100
3.3999-30.4740.16671440.14325964X-RAY DIFFRACTION100

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