Header list of 1bds.pdb file
Complete list - 29 201 Bytes
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
Complete list - 29 201 Bytes