HEADER NEUROPEPTIDE 23-FEB-21 7LUW TITLE STRUCTURAL STUDIES ABOUT SCNTX NEUROTOXIN USING SOLUTION NMR 2D AND 3D COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHORT-CHAIN NEUROTOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXINS, NEUROTOXIN, SCNTX, NEUROPEPTIDE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.DEL RIO-PORTILLA,A.E.LOPEZ-GIRALDO REVDAT 3 09-OCT-24 7LUW 1 REMARK REVDAT 2 14-JUN-23 7LUW 1 REMARK REVDAT 1 14-APR-21 7LUW 0 JRNL AUTH F.DEL RIO-PORTILLA,A.E.LOPEZ-GIRALDO JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE NEUROTOXIN SCNTX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 16 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254889. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM SCNTX NEUROTOXIN, 95% REMARK 210 H2O/5% D2O; 0.7 MM [U-100% 13C; REMARK 210 U-100% 15N, 1H] SCNTX NEUROTOXIN, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 3D H(CCO)NH; 3D REMARK 210 HCCH-TOCSY; 3D C(CO)NH; 3D HNCA; REMARK 210 3D HNCACB; 3D HNCO; 2D 1H-13C REMARK 210 HSQC; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, CARA 1.5, NMRFAM REMARK 210 -SPARKY, TALOS N REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 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 1 TYR A 39 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 ARG A 53 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 CYS A 74 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 2 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 ARG A 53 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 CYS A 74 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 3 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 53 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 CYS A 69 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 3 CYS A 74 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 4 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 ARG A 53 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 6 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 9 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 10 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 11 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 CYS A 74 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 13 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 13 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 14 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 14 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 69 ANGLE DEVIATIONS. 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 1 ASN A 21 25.63 -145.53 REMARK 500 1 SER A 24 -2.54 -55.69 REMARK 500 1 PRO A 28 96.05 -55.36 REMARK 500 1 SER A 34 42.92 -140.15 REMARK 500 1 CYS A 57 45.14 -147.02 REMARK 500 1 ASP A 72 -132.92 42.14 REMARK 500 2 ILE A 18 41.00 -103.22 REMARK 500 2 TYR A 20 -169.85 -72.95 REMARK 500 2 ASN A 21 24.25 -176.21 REMARK 500 2 SER A 25 46.42 -147.67 REMARK 500 2 TYR A 39 -179.87 53.78 REMARK 500 2 ASP A 72 -93.76 -52.45 REMARK 500 2 LYS A 73 4.43 -65.30 REMARK 500 3 HIS A 5 35.97 -78.47 REMARK 500 3 HIS A 8 34.18 -88.48 REMARK 500 3 GLU A 14 73.65 -105.40 REMARK 500 3 ASN A 21 21.45 -154.88 REMARK 500 3 ASP A 72 -75.14 -55.40 REMARK 500 4 ASN A 21 37.75 -155.23 REMARK 500 4 SER A 24 2.74 -62.16 REMARK 500 4 ASP A 45 -153.86 -153.50 REMARK 500 5 ASN A 21 0.34 51.49 REMARK 500 5 PRO A 28 108.86 -56.43 REMARK 500 5 TYR A 39 160.62 55.58 REMARK 500 5 ASP A 72 -105.60 -49.10 REMARK 500 6 ASN A 21 -6.92 59.13 REMARK 500 6 PRO A 28 98.13 -65.27 REMARK 500 6 ASP A 45 -139.72 -129.81 REMARK 500 9 HIS A 8 52.87 -93.36 REMARK 500 9 ASN A 21 10.58 51.93 REMARK 500 9 CYS A 57 39.89 -152.96 REMARK 500 9 ASP A 72 -76.75 -63.68 REMARK 500 10 HIS A 5 1.75 -67.15 REMARK 500 10 ASN A 21 12.77 52.61 REMARK 500 10 ARG A 47 5.55 -67.34 REMARK 500 10 ARG A 53 87.25 -159.24 REMARK 500 10 CYS A 57 60.75 -118.49 REMARK 500 10 ASP A 72 -77.88 -61.21 REMARK 500 11 HIS A 10 13.58 54.33 REMARK 500 11 GLU A 14 42.55 -84.39 REMARK 500 11 ARG A 47 10.96 -68.49 REMARK 500 11 ARG A 53 121.28 -171.90 REMARK 500 11 ASP A 72 -75.36 -61.11 REMARK 500 12 HIS A 8 44.09 -77.79 REMARK 500 12 ASN A 21 18.57 39.17 REMARK 500 12 SER A 25 -26.92 -140.93 REMARK 500 12 THR A 29 -168.33 -113.09 REMARK 500 12 ASP A 72 -85.08 -71.60 REMARK 500 13 ASN A 21 10.55 50.33 REMARK 500 13 ASP A 72 -77.33 -53.97 REMARK 500 REMARK 500 THIS ENTRY HAS 73 RAMACHANDRAN OUTLIERS. 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 1 TYR A 39 0.15 SIDE CHAIN REMARK 500 1 ARG A 53 0.11 SIDE CHAIN REMARK 500 2 TYR A 20 0.10 SIDE CHAIN REMARK 500 3 TYR A 20 0.07 SIDE CHAIN REMARK 500 4 ARG A 53 0.08 SIDE CHAIN REMARK 500 6 HIS A 46 0.10 SIDE CHAIN REMARK 500 7 TYR A 20 0.14 SIDE CHAIN REMARK 500 8 ARG A 16 0.10 SIDE CHAIN REMARK 500 9 TYR A 20 0.10 SIDE CHAIN REMARK 500 10 TYR A 20 0.07 SIDE CHAIN REMARK 500 10 ARG A 53 0.09 SIDE CHAIN REMARK 500 11 TYR A 20 0.12 SIDE CHAIN REMARK 500 12 TYR A 39 0.07 SIDE CHAIN REMARK 500 12 ARG A 53 0.09 SIDE CHAIN REMARK 500 17 TYR A 20 0.09 SIDE CHAIN REMARK 500 17 ARG A 53 0.17 SIDE CHAIN REMARK 500 20 TYR A 20 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30867 RELATED DB: BMRB REMARK 900 STRUCTURAL STUDIES ABOUT SCNTX NEUROTOXIN USING SOLUTION NMR 2D AND REMARK 900 3D DBREF 7LUW A 1 76 PDB 7LUW 7LUW 1 76 SEQRES 1 A 76 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ILE SEQRES 2 A 76 GLU GLY ARG MET ILE CYS TYR ASN GLN GLN SER SER GLN SEQRES 3 A 76 PRO PRO THR THR LYS THR CYS SER GLU THR SER CYS TYR SEQRES 4 A 76 LYS LYS THR TRP ARG ASP HIS ARG GLY THR ILE ILE GLU SEQRES 5 A 76 ARG GLY CYS GLY CYS PRO LYS VAL LYS PRO GLY ILE LYS SEQRES 6 A 76 LEU HIS CYS CYS ARG THR ASP LYS CYS ASN ASN SHEET 1 AA1 2 ILE A 18 TYR A 20 0 SHEET 2 AA1 2 THR A 30 THR A 32 -1 O LYS A 31 N CYS A 19 SHEET 1 AA2 3 GLY A 48 GLU A 52 0 SHEET 2 AA2 3 CYS A 38 ASP A 45 -1 N ASP A 45 O GLY A 48 SHEET 3 AA2 3 HIS A 67 CYS A 69 -1 O CYS A 69 N CYS A 38 SSBOND 1 CYS A 19 CYS A 38 1555 1555 2.03 SSBOND 2 CYS A 33 CYS A 55 1555 1555 2.03 SSBOND 3 CYS A 57 CYS A 68 1555 1555 2.03 SSBOND 4 CYS A 69 CYS A 74 1555 1555 2.04 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 MODEL 1