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- PDB-1bds: DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE ... -

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Entry
Database: PDB / ID: 1bds
TitleDETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE ANTIHYPERTENSIVE AND ANTIVIRAL PROTEIN BDS-I FROM THE SEA ANEMONE ANEMONIA SULCATA. A STUDY USING NUCLEAR MAGNETIC RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
ComponentsBDS-I
KeywordsANTI-HYPERTENSIVE / ANTI-VIRAL PROTEIN
Function / homology
Function and homology information


nematocyst / ion channel inhibitor activity / sodium channel regulator activity / potassium channel regulator activity / regulation of blood pressure / toxin activity / extracellular region
Similarity search - Function
BDS potassium channel toxin / Potassium-channel blocking toxin / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Delta/kappa-actitoxin-Avd4a
Similarity search - Component
Biological speciesAnemonia sulcata (snake-locks sea anemone)
MethodSOLUTION NMR
AuthorsClore, G.M. / Driscoll, P.C. / Gronenborn, A.M.
Citation
Journal: Biochemistry / Year: 1989
Title: Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance ...Title: Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.
Authors: Driscoll, P.C. / Gronenborn, A.M. / Beress, L. / Clore, G.M.
#1: Journal: Biochemistry / Year: 1989
Title: A Proton Nuclear Magnetic Resonance Study of the Antihypertensive and Antiviral Protein Bds-I from the Sea Anemone Anemonia Sulcata. Sequential and Stereospecific Resonance Assignment and Secondary Structure
Authors: Driscoll, P.C. / Clore, G.M. / Beress, L. / Gronenborn, A.M.
#2: Journal: FEBS Lett. / Year: 1989
Title: The Influence of Stereospecific Assignments on the Determination of Three-Dimensional Structures of Proteins by Nuclear Magnetic Resonance Spectroscopy. Application to the Sea Anemone Protein Bds-I
Authors: Driscoll, P.C. / Gronenborn, A.M. / Clore, G.M.
History
DepositionNov 14, 1988Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BDS-I


Theoretical massNumber of molelcules
Total (without water)4,7191
Polymers4,7191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: RESIDUES PRO 36 AND PRO 42 ARE CIS PROLINES.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide BDS-I


Mass: 4719.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anemonia sulcata (snake-locks sea anemone)
References: UniProt: P11494
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: XPLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, ...Details: REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229, 317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER, YALE UNIVERSITY, CT 06511). STRUCTURAL STATISTICS RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)* RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS) ALL 513 0.079 INTERRESIDUE SHORT RANGE 150 0.086 INTERRESIDUE LONG RANGE 105 0.100 INTRARESIDUE 234 0.065 HBOND *(2)* 24 0.043 POTENTIAL ENERGY TERMS TYPE ENERGY (KCAL/MOL) F(NOE) *(3)* 160 F(TOR) *(4)* 24 F(REPEL) *(5)* 72 LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS -117 KCAL/MOL. DEVIATIONS FROM IDEALIZED GEOMETRY *(6)* TYPE TOTAL NUMBER RMS DEVIATION BONDS 646 0.013 (ANGSTROMS) ANGLES 1157 2.517 (DEGREES) IMPROPERS 242 0.797 (DEGREES) NOTES. *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS ARE CALCULATED WITH RESPECT TO THE UPPER AND LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN 0.5 ANGSTROMS. *(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII OF THE RELEVANT ATOMS. *(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF 50 KCAL/MOL/ANGSTROM**2. *(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO RESTRICT THE RANGES OF 23 PHI AND 21 CHI1 TORSION ANGLES, AND THE OMEGA PEPTIDE BOND TORSION ANGLES OF THE FIVE PROLINE RESIDUES (PRO 36 AND 42 BEING RESTRAINED TO THE CIS CONFORMATION AND THE OTHERS TO TRANS). *(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY FUNCTION. *(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION OF PROLINES) IN THE TRANS CONFORMATION. IN THE DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED IN THE BOND AND ANGLE TERMS. A TOTAL OF 42 STRUCTURES CONSISTENT WITH THE NMR DATA WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THESE 42 STRUCTURES ARE GIVEN IN THE PDB ENTRY *2BDS*. THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS ARE AVAILABLE IN THE PDB NMR RESTRAINT FILE.
NMR ensembleConformers submitted total number: 1

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