HEADER ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN 14-NOV-88 1BDS TITLE DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE TITLE 2 ANTIHYPERTENSIVE AND ANTIVIRAL PROTEIN BDS-I FROM THE SEA ANEMONE TITLE 3 ANEMONIA SULCATA. A STUDY USING NUCLEAR MAGNETIC RESONANCE AND HYBRID TITLE 4 DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING COMPND MOL_ID: 1; COMPND 2 MOLECULE: BDS-I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANEMONIA SULCATA; SOURCE 3 ORGANISM_COMMON: SNAKE-LOCKS SEA ANEMONE; SOURCE 4 ORGANISM_TAXID: 6108 KEYWDS ANTI-HYPERTENSIVE, ANTI-VIRAL PROTEIN EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,P.C.DRISCOLL,A.M.GRONENBORN REVDAT 8 29-NOV-17 1BDS 1 REMARK HELIX REVDAT 7 24-FEB-09 1BDS 1 VERSN REVDAT 6 01-APR-03 1BDS 1 JRNL REVDAT 5 31-JAN-94 1BDS 1 REMARK REVDAT 4 15-APR-92 1BDS 1 EXPDTA REVDAT 3 15-OCT-89 1BDS 1 AUTHOR EXPDTA REVDAT 2 12-JUL-89 1BDS 1 JRNL REMARK REVDAT 1 09-JAN-89 1BDS 0 JRNL AUTH P.C.DRISCOLL,A.M.GRONENBORN,L.BERESS,G.M.CLORE JRNL TITL DETERMINATION OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF JRNL TITL 2 THE ANTIHYPERTENSIVE AND ANTIVIRAL PROTEIN BDS-I FROM THE JRNL TITL 3 SEA ANEMONE ANEMONIA SULCATA: A STUDY USING NUCLEAR MAGNETIC JRNL TITL 4 RESONANCE AND HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED JRNL TITL 5 ANNEALING. JRNL REF BIOCHEMISTRY V. 28 2188 1989 JRNL REFN ISSN 0006-2960 JRNL PMID 2566326 JRNL DOI 10.1021/BI00431A033 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.C.DRISCOLL,G.M.CLORE,L.BERESS,A.M.GRONENBORN REMARK 1 TITL A PROTON NUCLEAR MAGNETIC RESONANCE STUDY OF THE REMARK 1 TITL 2 ANTIHYPERTENSIVE AND ANTIVIRAL PROTEIN BDS-I FROM THE SEA REMARK 1 TITL 3 ANEMONE ANEMONIA SULCATA. SEQUENTIAL AND STEREOSPECIFIC REMARK 1 TITL 4 RESONANCE ASSIGNMENT AND SECONDARY STRUCTURE REMARK 1 REF BIOCHEMISTRY V. 28 2178 1989 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.C.DRISCOLL,A.M.GRONENBORN,G.M.CLORE REMARK 1 TITL THE INFLUENCE OF STEREOSPECIFIC ASSIGNMENTS ON THE REMARK 1 TITL 2 DETERMINATION OF THREE-DIMENSIONAL STRUCTURES OF PROTEINS BY REMARK 1 TITL 3 NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY. APPLICATION TO THE REMARK 1 TITL 4 SEA ANEMONE PROTEIN BDS-I REMARK 1 REF FEBS LETT. V. 243 223 1989 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 REFINEMENT. THE METHOD USED TO DETERMINE AND REFINE THE REMARK 3 STRUCTURE IS THE HYBRID METRIC MATRIX DISTANCE REMARK 3 GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD REMARK 3 (M.NILGES, G.M.CLORE, A.M. GRONENBORN, FEBS LETT. 229, REMARK 3 317-324 (1988)) USING THE PROGRAM XPLOR (A.T. BRUENGER, REMARK 3 YALE UNIVERSITY, CT 06511). REMARK 3 REMARK 3 STRUCTURAL STATISTICS REMARK 3 REMARK 3 RMS DEVIATION FROM EXPERIMENTAL RESTRAINTS *(1)* REMARK 3 REMARK 3 RESTRAINT TYPE NUMBER OF RESTRAINTS RMS (ANGSTROMS) REMARK 3 REMARK 3 ALL 513 0.079 REMARK 3 INTERRESIDUE REMARK 3 SHORT RANGE 150 0.086 REMARK 3 INTERRESIDUE REMARK 3 LONG RANGE 105 0.100 REMARK 3 INTRARESIDUE 234 0.065 REMARK 3 HBOND *(2)* 24 0.043 REMARK 3 REMARK 3 POTENTIAL ENERGY TERMS REMARK 3 REMARK 3 TYPE ENERGY (KCAL/MOL) REMARK 3 REMARK 3 F(NOE) *(3)* 160 REMARK 3 F(TOR) *(4)* 24 REMARK 3 F(REPEL) *(5)* 72 REMARK 3 REMARK 3 LENNARD-JONES VAN DER WAALS ENERGY (E(L-J)) CALCULATED REMARK 3 USING THE *CHARMM* EMPIRICAL ENERGY FUNCTION IS REMARK 3 -117 KCAL/MOL. REMARK 3 REMARK 3 DEVIATIONS FROM IDEALIZED GEOMETRY *(6)* REMARK 3 REMARK 3 TYPE TOTAL NUMBER RMS DEVIATION REMARK 3 REMARK 3 BONDS 646 0.013 (ANGSTROMS) REMARK 3 ANGLES 1157 2.517 (DEGREES) REMARK 3 IMPROPERS 242 0.797 (DEGREES) REMARK 3 REMARK 3 NOTES. REMARK 3 *(1)* THE RMS DEVIATION FROM THE EXPERIMENTAL RESTRAINTS REMARK 3 ARE CALCULATED WITH RESPECT TO THE UPPER AND REMARK 3 LOWER LIMITS OF THE DISTANCE RESTRAINTS. NONE OF REMARK 3 THE STRUCTURES EXHIBITED VIOLATIONS GREATER THAN REMARK 3 0.5 ANGSTROMS. REMARK 3 *(2)* FOR EACH BACKBONE HYDROGEN BOND THERE ARE TWO REMARK 3 RESTRAINTS - R(NH-O) .LT. 2.3 ANGSTROMS AND REMARK 3 R(N-O) .LT. 3.3 ANGSTROMS. THE LOWER LIMITS REMARK 3 ARE GIVEN BY THE SUM OF THE VAN DER WAALS RADII REMARK 3 OF THE RELEVANT ATOMS. REMARK 3 *(3)* THE VALUES OF THE SQUARE-WELL NOE POTENTIAL REMARK 3 F(NOE) ARE CALCULATED WITH A FORCE CONSTANT OF REMARK 3 50 KCAL/MOL/ANGSTROM**2. REMARK 3 *(4)* THE VALUES OF F(PHI) ARE CALCULATED WITH A FORCE REMARK 3 CONSTANT OF 200 KCAL/MOL/RAD**2. F(PHI) IS A REMARK 3 SQUARE-WELL DIHEDRAL POTENTIAL WHICH IS USED TO REMARK 3 RESTRICT THE RANGES OF 23 PHI AND 21 CHI1 TORSION REMARK 3 ANGLES, AND THE OMEGA PEPTIDE BOND TORSION ANGLES REMARK 3 OF THE FIVE PROLINE RESIDUES (PRO 36 AND 42 BEING REMARK 3 RESTRAINED TO THE CIS CONFORMATION AND THE OTHERS REMARK 3 TO TRANS). REMARK 3 *(5)* THE VALUE OF THE VAN DER WAALS REPULSION TERM REMARK 3 F(REPEL) IS CALCULATED WITH A FORCE CONSTANT OF REMARK 3 4 KCAL/MOL/ANGSTROM**4 WITH THE HARD SPHERE REMARK 3 VAN DER WAALS RADII SET TO 0.8 TIMES THE STANDARD REMARK 3 VALUES USED IN THE *CHARMM* EMPIRICAL ENERGY REMARK 3 FUNCTION. REMARK 3 *(6)* THE IMPROPER TERMS SERVE TO MAINTAIN PLANARITY REMARK 3 AND APPROPRIATE CHIRALITY. THEY ALSO MAINTAIN THE REMARK 3 PEPTIDE BONDS OF ALL RESIDUES (WITH THE EXCEPTION REMARK 3 OF PROLINES) IN THE TRANS CONFORMATION. IN THE REMARK 3 DYNAMICAL SIMULATED ANNEALING CALCULATIONS, THE REMARK 3 RESTRAINTS FOR THE DISULFIDE BRIDGES ARE INCLUDED REMARK 3 IN THE BOND AND ANGLE TERMS. REMARK 3 REMARK 3 A TOTAL OF 42 STRUCTURES CONSISTENT WITH THE NMR DATA REMARK 3 WERE CALCULATED. THIS ENTRY REPRESENTS THE COORDINATES REMARK 3 OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL REMARK 3 STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO REMARK 3 FURTHER RESTRAINED MINIMIZATION. THE COORDINATES OF THESE REMARK 3 42 STRUCTURES ARE GIVEN IN THE PDB ENTRY *2BDS*. REMARK 3 REMARK 3 THE THERMAL PARAMETERS GIVEN IN THIS ENTRY REPRESENT THE REMARK 3 ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT REMARK 3 THE MEAN COORDINATE POSITIONS. REMARK 3 REMARK 3 ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS REMARK 3 ARE AVAILABLE IN THE PDB NMR RESTRAINT FILE. REMARK 4 REMARK 4 1BDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171634. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 16 CG TRP A 16 CD2 -0.129 REMARK 500 TRP A 35 CG TRP A 35 CD2 -0.114 REMARK 500 HIS A 43 CG HIS A 43 ND1 -0.125 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TRP A 16 CD1 - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 TRP A 16 CG - CD1 - NE1 ANGL. DEV. = -7.2 DEGREES REMARK 500 TRP A 16 CD1 - NE1 - CE2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP A 16 NE1 - CE2 - CZ2 ANGL. DEV. = 10.1 DEGREES REMARK 500 TRP A 16 NE1 - CE2 - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 TRP A 16 CG - CD2 - CE3 ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP A 35 CG - CD1 - NE1 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 35 NE1 - CE2 - CZ2 ANGL. DEV. = 9.4 DEGREES REMARK 500 TRP A 35 NE1 - CE2 - CD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 3 20.70 -78.66 REMARK 500 PRO A 10 -161.55 -67.48 REMARK 500 ILE A 17 -153.52 -94.78 REMARK 500 LEU A 18 78.73 -67.72 REMARK 500 THR A 29 -38.20 -160.53 REMARK 500 PRO A 36 39.10 -78.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 1 ALA A 2 -149.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 12 0.30 SIDE CHAIN REMARK 500 ARG A 19 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BDS RELATED DB: PDB DBREF 1BDS A 1 43 UNP P11494 BDS1_ANESU 1 43 SEQRES 1 A 43 ALA ALA PRO CYS PHE CYS SER GLY LYS PRO GLY ARG GLY SEQRES 2 A 43 ASP LEU TRP ILE LEU ARG GLY THR CYS PRO GLY GLY TYR SEQRES 3 A 43 GLY TYR THR SER ASN CYS TYR LYS TRP PRO ASN ILE CYS SEQRES 4 A 43 CYS TYR PRO HIS SHEET 1 A 3 ASP A 14 ILE A 17 0 SHEET 2 A 3 ASN A 37 TYR A 41 -1 SHEET 3 A 3 SER A 30 LYS A 34 -1 SSBOND 1 CYS A 4 CYS A 39 1555 1555 2.02 SSBOND 2 CYS A 6 CYS A 32 1555 1555 2.03 SSBOND 3 CYS A 22 CYS A 40 1555 1555 2.02 CISPEP 1 TRP A 35 PRO A 36 0 -7.56 CISPEP 2 TYR A 41 PRO A 42 0 6.48 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000