HEADER NEUROTOXIN 08-APR-97 1AHO TITLE THE AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A SCORPION TITLE 2 PROTEIN TOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN II; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANDROCTONUS AUSTRALIS; SOURCE 3 ORGANISM_TAXID: 70175; SOURCE 4 STRAIN: HECTOR KEYWDS TOXIN II, SCORPION, AB INITIO PHASING, NEUROTOXIN EXPDTA X-RAY DIFFRACTION AUTHOR G.D.SMITH,R.H.BLESSING,S.E.EALICK,J.C.FONTECILLA-CAMPS,H.A.HAUPTMAN, AUTHOR 2 D.HOUSSET,D.A.LANGS,R.MILLER REVDAT 6 30-OCT-24 1AHO 1 REMARK REVDAT 5 05-JUN-24 1AHO 1 REMARK REVDAT 4 13-JUL-11 1AHO 1 VERSN REVDAT 3 24-FEB-09 1AHO 1 VERSN REVDAT 2 01-NOV-99 1AHO 1 JRNL REVDAT 1 15-OCT-97 1AHO 0 JRNL AUTH G.D.SMITH,R.H.BLESSING,S.E.EALICK,J.C.FONTECILLA-CAMPS, JRNL AUTH 2 H.A.HAUPTMAN,D.HOUSSET,D.A.LANGS,R.MILLER JRNL TITL AB INITIO STRUCTURE DETERMINATION AND REFINEMENT OF A JRNL TITL 2 SCORPION PROTEIN TOXIN. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 53 551 1997 JRNL REFN ISSN 0907-4449 JRNL PMID 15299886 JRNL DOI 10.1107/S0907444997005386 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.HOUSSET,C.HABERSETZER-ROCHAT,J.P.ASTIER, REMARK 1 AUTH 2 J.C.FONTECILLA-CAMPS REMARK 1 TITL CRYSTAL STRUCTURE OF TOXIN II FROM THE SCORPION ANDROCTONUS REMARK 1 TITL 2 AUSTRALIS HECTOR REFINED AT 1.3 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 238 88 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.C.FONTECILLA-CAMPS,C.HABERSETZER-ROCHAT,H.ROCHAT REMARK 1 TITL ORTHORHOMBIC CRYSTALS AND THREE-DIMENSIONAL STRUCTURE OF THE REMARK 1 TITL 2 POTENT TOXIN II FROM THE SCORPION ANDROCTONUS AUSTRALIS REMARK 1 TITL 3 HECTOR REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 85 7443 1988 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 30609 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.158 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) : 0.1630 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) : 31001 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 500 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.72 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) : 0.014 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.041 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : 0.011 ; 0.030 REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.041 ; 0.050 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.127 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.192 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.201 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : 0.148 ; 0.500 REMARK 3 H-BOND (X-H...Y) (A) : 0.485 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.900 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 12.600; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 19.500; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.106 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.523 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.692 ; 1.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.370 ; 2.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE WAS REFINED INITIALLY WITH X-PLOR TO A RESIDUAL OF REMARK 3 0.203 (25509 REFLECTIONS) AND A FREE R OF 0.224 (2830 REFLECTIONS) REMARK 3 . PROFFT (FINZEL), MODIFIED TO INCORPORATE A TWO LINE WEIGHTING REMARK 3 SCHEME (SMITH), WAS USED TO PERFORM THE FINAL REFINEMENTS REMARK 3 INCLUDING CONTRIBUTIONS FROM HYDROGEN ATOMS. REMARK 3 REMARK 3 DISORDERED RESIDUES WERE IDENTIFIED GRAPHICALLY. REMARK 4 REMARK 4 1AHO 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_1000170828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-94 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NA REMARK 200 OPTICS : NA REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ROTAVATA, AGROVATA, MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (AGROVATA, ROTAVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31001 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.964 REMARK 200 RESOLUTION RANGE LOW (A) : 16.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT METHODS REMARK 200 SOFTWARE USED: SHAKE-N-BAKE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.8 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 22.95000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.05000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.05000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.95000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.35000 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 9 OD2 REMARK 470 LYS A 30 CD CE NZ REMARK 470 LYS A 50 NZ 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 ASN A 11 33.12 73.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 1AHO A 1 64 UNP P01484 SCX2_ANDAU 20 83 SEQRES 1 A 64 VAL LYS ASP GLY TYR ILE VAL ASP ASP VAL ASN CYS THR SEQRES 2 A 64 TYR PHE CYS GLY ARG ASN ALA TYR CYS ASN GLU GLU CYS SEQRES 3 A 64 THR LYS LEU LYS GLY GLU SER GLY TYR CYS GLN TRP ALA SEQRES 4 A 64 SER PRO TYR GLY ASN ALA CYS TYR CYS TYR LYS LEU PRO SEQRES 5 A 64 ASP HIS VAL ARG THR LYS GLY PRO GLY ARG CYS HIS FORMUL 2 HOH *129(H2 O) HELIX 1 1 ASN A 19 LYS A 28 1 10 SHEET 1 A 2 SER A 33 GLN A 37 0 SHEET 2 A 2 ALA A 45 TYR A 49 -1 N TYR A 49 O SER A 33 SSBOND 1 CYS A 12 CYS A 63 1555 1555 2.01 SSBOND 2 CYS A 16 CYS A 36 1555 1555 2.03 SSBOND 3 CYS A 22 CYS A 46 1555 1555 2.03 SSBOND 4 CYS A 26 CYS A 48 1555 1555 2.01 CRYST1 45.900 40.700 30.100 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 0.021786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024570 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033223 0.00000