HEADER TOXIN (HEMOLYTIC POLYPEPTIDE) 04-OCT-90 2MLT TITLE MELITTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MELITTIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APIS MELLIFERA; SOURCE 3 ORGANISM_COMMON: HONEY BEE; SOURCE 4 ORGANISM_TAXID: 7460 KEYWDS TOXIN (HEMOLYTIC POLYPEPTIDE) EXPDTA X-RAY DIFFRACTION AUTHOR D.EISENBERG,M.GRIBSKOV,T.C.TERWILLIGER REVDAT 6 05-JUN-24 2MLT 1 REMARK LINK REVDAT 5 16-NOV-11 2MLT 1 HETATM REVDAT 4 13-JUL-11 2MLT 1 VERSN REVDAT 3 24-FEB-09 2MLT 1 VERSN REVDAT 2 15-JUL-92 2MLT 1 SPRSDE REVDAT 1 15-OCT-90 2MLT 0 SPRSDE 15-OCT-90 2MLT 1MLT JRNL AUTH M.GRIBSKOV,L.WESSON,D.EISENBERG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.C.TERWILLIGER,D.EISENBERG REMARK 1 TITL THE STRUCTURE OF MELITTIN. I. STRUCTURE DETERMINATION AND REMARK 1 TITL 2 PARTIAL REFINEMENT. REMARK 1 REF J.BIOL.CHEM. V. 257 6010 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.C.TERWILLIGER,D.EISENBERG REMARK 1 TITL THE STRUCTURE OF MELITTIN. II. INTERPRETATION OF THE REMARK 1 TITL 2 STRUCTURE REMARK 1 REF J.BIOL.CHEM. V. 257 6016 1982 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.ANDERSON,T.C.TERWILLIGER,W.WICKNER,D.EISENBERG REMARK 1 TITL MELITTIN FORMS CRYSTALS WHICH ARE SUITABLE FOR HIGH REMARK 1 TITL 2 RESOLUTION X-RAY STRUCTURAL ANALYSIS AND WHICH REVEAL A REMARK 1 TITL 3 MOLECULAR 2-FOLD AXIS OF SYMMETRY REMARK 1 REF J.BIOL.CHEM. V. 255 2578 1980 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 137 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) : 0.198 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 : 402 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 23 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) : 0.026 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.046 ; 0.030 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.073 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.016 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.244 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.189 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.209 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : 0.544 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.079 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.913 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.043 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.281 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MLT 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_1000178373. 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 (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.10550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.10550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.41600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.14650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.41600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.14650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.10550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.41600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 19.14650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 21.10550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.41600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 19.14650 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 42.21100 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 36 LIES ON A SPECIAL POSITION. 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 VAL A 5 CA - CB - CG2 ANGL. DEV. = 9.2 DEGREES REMARK 500 LEU A 6 CB - CA - C ANGL. DEV. = 11.6 DEGREES REMARK 500 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 GLN A 26 CA - C - O ANGL. DEV. = -14.7 DEGREES REMARK 500 ARG B 22 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 GLN B 25 CB - CG - CD ANGL. DEV. = 18.1 DEGREES REMARK 500 GLN B 26 O - C - N ANGL. DEV. = 10.6 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 THR A 11 -41.83 -130.92 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 SO4 B 28 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 29 DBREF 2MLT A 1 26 UNP P01501 MEL_APIME 44 69 DBREF 2MLT B 1 26 UNP P01501 MEL_APIME 44 69 SEQRES 1 A 27 GLY ILE GLY ALA VAL LEU LYS VAL LEU THR THR GLY LEU SEQRES 2 A 27 PRO ALA LEU ILE SER TRP ILE LYS ARG LYS ARG GLN GLN SEQRES 3 A 27 NH2 SEQRES 1 B 27 GLY ILE GLY ALA VAL LEU LYS VAL LEU THR THR GLY LEU SEQRES 2 B 27 PRO ALA LEU ILE SER TRP ILE LYS ARG LYS ARG GLN GLN SEQRES 3 B 27 NH2 HET NH2 A 27 1 HET NH2 B 27 1 HET SO4 B 28 5 HET SO4 B 29 5 HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION FORMUL 1 NH2 2(H2 N) FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *23(H2 O) HELIX 1 AA GLY A 1 THR A 11 1 11 HELIX 2 BA PRO A 14 GLN A 26 1 13 HELIX 3 AB GLY B 1 THR B 11 1 11 HELIX 4 BB PRO B 14 GLN B 26 1 13 LINK C GLN A 26 N NH2 A 27 1555 1555 1.32 LINK C GLN B 26 N NH2 B 27 1555 1555 1.30 SITE 1 AC1 4 ILE A 2 GLY A 3 TRP A 19 ARG B 24 SITE 1 AC2 7 ARG A 24 ILE B 2 GLY B 3 TRP B 19 SITE 2 AC2 7 LYS B 23 ARG B 24 HOH B 31 CRYST1 60.832 38.293 42.211 90.00 90.00 90.00 C 2 2 21 16 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 0.016439 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023691 0.00000 MTRIX1 1 -0.996310 -0.033870 -0.078870 71.25100 1 MTRIX2 1 0.048050 -0.981470 -0.185470 2.71100 1 MTRIX3 1 -0.071130 -0.188580 0.979480 2.05300 1