HEADER TOXIN 20-FEB-92 2SN3 TITLE STRUCTURE OF SCORPION TOXIN VARIANT-3 AT 1.2 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCORPION NEUROTOXIN (VARIANT 3); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CENTRUROIDES EXILICAUDA; SOURCE 3 ORGANISM_TAXID: 6879 KEYWDS TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHAO,M.CARSON,S.E.EALICK,C.E.BUGG REVDAT 4 29-NOV-17 2SN3 1 HELIX REVDAT 3 24-FEB-09 2SN3 1 VERSN REVDAT 2 01-APR-03 2SN3 1 JRNL REVDAT 1 31-JAN-94 2SN3 0 SPRSDE 31-JAN-94 2SN3 1SN3 JRNL AUTH B.ZHAO,M.CARSON,S.E.EALICK,C.E.BUGG JRNL TITL STRUCTURE OF SCORPION TOXIN VARIANT-3 AT 1.2 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 227 239 1992 JRNL REFN ISSN 0022-2836 JRNL PMID 1522588 JRNL DOI 10.1016/0022-2836(92)90694-F REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.J.ALMASSY,J.C.FONTECILLA-CAMPS,F.L.SUDDATH,C.E.BUGG REMARK 1 TITL STRUCTURE OF VARIANT-3 SCORPION NEUROTOXIN FROM CENTRUROIDES REMARK 1 TITL 2 SCULPTURATUS EWING, REFINED AT 1.8 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 170 497 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.C.FONTECILLA-CAMPS,R.J.ALMASSY,S.E.EALICK,F.L.SUDDATH, REMARK 1 AUTH 2 D.D.WATT,R.J.FELDMANN,C.E.BUGG REMARK 1 TITL ARCHITECTURE OF SCORPION NEUROTOXINS. A CLASS OF REMARK 1 TITL 2 MEMBRANE-BINDING PROTEINS REMARK 1 REF TRENDS BIOCHEM.SCI.(PERS. V. 6 291 1981 REMARK 1 REF 2 ED.) REMARK 1 REFN ISSN 0376-5067 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.C.FONTECILLA-CAMPS,R.J.ALMASSY,F.L.SUDDATH,D.D.WATT, REMARK 1 AUTH 2 C.E.BUGG REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF A PROTEIN FROM SCORPION REMARK 1 TITL 2 VENOM. A NEW STRUCTURAL CLASS OF NEUROTOXINS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 77 6496 1980 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 492 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.024 ; 0.030 REMARK 3 ANGLE DISTANCE (A) : 0.041 ; 0.060 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.052 ; 0.070 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.018 ; 0.040 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.145 ; 0.200 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.191 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.463 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.406 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 6.200 ; NULL REMARK 3 STAGGERED (DEGREES) : 13.100; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2SN3 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_1000178634. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 26.03500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.16000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.16000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.97000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HD2 TYR A 38 O HOH A 171 1.55 REMARK 500 CD2 TYR A 38 O HOH A 171 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 2 CD GLU A 2 OE1 0.098 REMARK 500 CYS A 12 CB CYS A 12 SG 0.176 REMARK 500 GLU A 28 CD GLU A 28 OE2 0.093 REMARK 500 GLU A 49 CD GLU A 49 OE1 0.069 REMARK 500 CYS A 65 CB CYS A 65 SG 0.431 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 LYS A 1 CA - CB - CG ANGL. DEV. = 17.3 DEGREES REMARK 500 GLU A 2 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 GLU A 2 CG - CD - OE2 ANGL. DEV. = 12.0 DEGREES REMARK 500 TYR A 4 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 CYS A 12 CA - CB - SG ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP A 26 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TYR A 42 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR A 42 CB - CG - CD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 PRO A 52 N - CD - CG ANGL. DEV. = 9.4 DEGREES REMARK 500 TYR A 58 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 58 CD1 - CE1 - CZ ANGL. DEV. = -5.5 DEGREES REMARK 500 CYS A 65 CA - CB - SG ANGL. DEV. = -15.8 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 GLN A 34 -52.36 -129.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 66 DBREF 2SN3 A 1 65 UNP P01494 SCX3_CENSC 1 65 SEQRES 1 A 65 LYS GLU GLY TYR LEU VAL LYS LYS SER ASP GLY CYS LYS SEQRES 2 A 65 TYR GLY CYS LEU LYS LEU GLY GLU ASN GLU GLY CYS ASP SEQRES 3 A 65 THR GLU CYS LYS ALA LYS ASN GLN GLY GLY SER TYR GLY SEQRES 4 A 65 TYR CYS TYR ALA PHE ALA CYS TRP CYS GLU GLY LEU PRO SEQRES 5 A 65 GLU SER THR PRO THR TYR PRO LEU PRO ASN LYS SER CYS HET MPD A 66 9 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD C6 H14 O2 FORMUL 3 HOH *125(H2 O) HELIX 1 H1 GLU A 23 LYS A 30 1 8 SHEET 1 S1 3 GLU A 2 VAL A 6 0 SHEET 2 S1 3 ALA A 45 GLU A 49 -1 O CYS A 48 N GLY A 3 SHEET 3 S1 3 TYR A 38 TYR A 42 -1 O TYR A 40 N TRP A 47 SSBOND 1 CYS A 12 CYS A 65 1555 1555 2.12 SSBOND 2 CYS A 16 CYS A 41 1555 1555 2.06 SSBOND 3 CYS A 25 CYS A 46 1555 1555 2.03 SSBOND 4 CYS A 29 CYS A 48 1555 1555 2.03 CISPEP 1 TYR A 58 PRO A 59 0 1.00 SITE 1 AC1 6 LYS A 8 ASN A 33 TYR A 40 TRP A 47 SITE 2 AC1 6 PRO A 56 HOH A 133 CRYST1 52.070 41.940 28.320 90.00 90.00 90.00 P 21 21 21 4 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 0.019205 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023844 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035311 0.00000